Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012584.1 Kokia drynarioides strain JFW-HI SEQ_127593, 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: 12492
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:988 original size:6 final size:6
Alignment explanation
Indices: 966--1003 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
956 TATTTTGGGT
* *
966 TTTTAA -TTTAA TATTAA TTTTAA TTTTAA TTTAAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1004 AAAGCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:988 original size:17 final size:17
Alignment explanation
Indices: 966--1005 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
956 TATTTTGGGT
966 TTTTAA-TTTAATATTAA
1 TTTTAATTTTAAT-TTAA
983 TTTTAATTTTAATTTAA
1 TTTTAATTTTAATTTAA
*
1000 ATTTAA
1 TTTTAA
1006 AGCAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATTTTAATTTAA
Found at i:1002 original size:12 final size:11
Alignment explanation
Indices: 966--1005 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
956 TATTTTGGGT
966 TTTTAATTTAA
1 TTTTAATTTAA
*
977 TATTAATTTTAA
1 TTTTAA-TTTAA
989 TTTTAATTTAA
1 TTTTAATTTAA
*
1000 ATTTAA
1 TTTTAA
1006 AGCAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:1004 original size:6 final size:6
Alignment explanation
Indices: 981--1073 Score: 66
Period size: 6 Copynumber: 15.5 Consensus size: 6
971 ATTTAATATT
* * ** **
981 AATTTT AATTTT AATTTA AATTTA AA-GCA AATTTA AATTTAAA AAGATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT--A AATTTA
**
1030 AATTTA AATTTA AGA--TA AATTTA AATTTA AAAATA AATTTA AAT
1 AATTTA AATTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA AAT
1074 CAATTTAAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
4 1 0.01
5 6 0.09
6 56 0.82
7 1 0.01
8 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:1013 original size:17 final size:18
Alignment explanation
Indices: 993--1073 Score: 112
Period size: 17 Copynumber: 4.5 Consensus size: 18
983 TTTTAATTTT
*
993 AATTTAAATTTAAAG-CA
1 AATTTAAATTTAAAGATA
1010 AATTTAAATTTAAAAAGATA
1 AATTTAAATTT--AAAGATA
1030 AATTTAAATTT-AAGATA
1 AATTTAAATTTAAAGATA
*
1047 AATTTAAATTTAAAAATA
1 AATTTAAATTTAAAGATA
1065 AATTTAAAT
1 AATTTAAAT
1074 CAATTTAAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
17 28 0.48
18 14 0.24
19 4 0.07
20 12 0.21
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (18 bp):
AATTTAAATTTAAAGATA
Found at i:1039 original size:37 final size:35
Alignment explanation
Indices: 993--1073 Score: 119
Period size: 37 Copynumber: 2.3 Consensus size: 35
983 TTTTAATTTT
993 AATTTAAATTTAA-AGCAAATTTAAATTTAAAAAGATA
1 AATTTAAATTTAAGA-CAAATTTAAATTT-AAAA-ATA
*
1030 AATTTAAATTTAAGATAAATTTAAATTTAAAAATA
1 AATTTAAATTTAAGACAAATTTAAATTTAAAAATA
1065 AATTTAAAT
1 AATTTAAAT
1074 CAATTTAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 12 0.29
36 4 0.10
37 25 0.60
38 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (35 bp):
AATTTAAATTTAAGACAAATTTAAATTTAAAAATA
Found at i:1773 original size:200 final size:200
Alignment explanation
Indices: 1456--1994 Score: 663
Period size: 200 Copynumber: 2.7 Consensus size: 200
1446 CCGTATCGCC
* * * * * * * * *
1456 TGTTTTAATTTGCTTCTTTGTGCCTCATCAGGAAGATGAATTTGGTTTACTTCTCAGTATTTCAT
1 TGTTTCAATCTGCTTCTCTGTACCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCAT
* *
1521 CAGGAAGCTAACCGTTTTATTGCTTCGA-CCTACTTCTCAGTATCTT-ATCAGGAAGTTGGGATT
66 CAGGAAGCTAACCTTTTTATTGCTTC-ACCCTGCTTCTCAGTAT-TTCATCAGGAAGTTGGG-TT
* *
1584 TGAAGATTTGCTCACATCGAGCC-CTGAGTCAGTATACTTCTCTGTATCTCATCAGGAAGATAAT
128 CGAAGATTTGCTCACATCGAGCCTC-GAGTCAGTATACTTCTCTGTATCTCATCAGGAAGATAAC
***
1648 CGCCCCGTT
192 CGCCCAACT
* * **
1657 TGTTTCAATCTGCTTCTCTGT-CCTTATCAGGAAGACGAATTTAGTTCACTTCTTTGTGTCTCAT
1 TGTTTCAATCTGCTTCTCTGTACCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCAT
* * * *
1721 CAGGATGCTAACCTTTTTATCGCTTCACCCTGCTTCTCAATATTTCATCAGGAAGCTGGGGTTCG
66 CAGGAAGCTAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATTTCATCAGGAAG-TTGGGTTCG
* * * ** * *
1786 AAGATTTGCTCGCATTGAGCTTCGAGTTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGC
130 AAGATTTGCTCACATCGAGCCTCGAGTCAGTATACTTCTCTGTATCTCATCAGGAAGATAACCGC
*
1851 CTAACT
195 CCAACT
* *
1857 TGTTTCAATCTGCTTCTCTGTACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCAT
1 TGTTTCAATCTGCTTCTCTGTACCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCAT
* * *
1922 CAGGAAGCTAACCTTTTTATTGCTTCACCTTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTCG
66 CAGGAAGCTAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATTTCATCAGGAAG-TTGGGTTCG
1987 AAGATTTG
130 AAGATTTG
1995 TTGGCATTGA
Statistics
Matches: 290, Mismatches: 43, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
199 3 0.01
200 161 0.56
201 126 0.43
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (200 bp):
TGTTTCAATCTGCTTCTCTGTACCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCAT
CAGGAAGCTAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATTTCATCAGGAAGTTGGGTTCGA
AGATTTGCTCACATCGAGCCTCGAGTCAGTATACTTCTCTGTATCTCATCAGGAAGATAACCGCC
CAACT
Found at i:1986 original size:201 final size:199
Alignment explanation
Indices: 1411--2005 Score: 717
Period size: 201 Copynumber: 3.0 Consensus size: 199
1401 TGTCGTTGAT
* * * ** * * * *
1411 TTGGTCTACTTCTTAGTATCTTATCAGGAAGATGACCGTATCGCCTGTTTTAATTTGCTTCTTTG
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATCTGCTTCTCTG
* * * * * *
1476 TGCCTCATCAGGAAGATGAATTTGGTTTACTTCTCAGTATTTCATCAGGAAGCTAACCGTTTTAT
66 T-CCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTAT
* * * * *
1541 TGCTTCGACCTACTTCTCAGTATCTTATCAGGAAG-TTGGGATTTGAAGATTTGCTCACATCGAG
130 TGCTTC-ACCTGCTTCTCAGTATCTCATCAGGAAGCTTGGG-TTCGAAGATTTGCTCGCATTGAG
1605 CCCTGAG
193 CCCTGAG
** * * * * *
1612 TCAGTATACTTCTCTGTATCTCATCAGGAAGATAATCGCCCCGTTTGTTTCAATCTGCTTCTCTG
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATCTGCTTCTCTG
* * ** * *
1677 TCCTTATCAGGAAGACGAATTTAGTTCACTTCTTTGTGTCTCATCAGGATGCTAACCTTTTTATC
66 TCCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATT
* * *
1742 GCTTCACCCTGCTTCTCAATATTTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAG-C
131 GCTTCA-CCTGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGCTCGCATTGAGCC
*
1806 TTCGAG
195 CT-GAG
**
1812 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGCCTAACTTGTTTCAATCTGCTTCTCTG
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATCTGCTTCTCTG
* *
1877 TACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTAT
66 T-CCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTAT
* * *
1942 TGCTTCACCTTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTCGAAGATTTGTTGGCATTGAG
130 TGCTTCACC-TGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGCTCGCATTGAG
2006 TTGGTATANT
Statistics
Matches: 330, Mismatches: 59, Indels: 10
0.83 0.15 0.03
Matches are distributed among these distances:
199 3 0.01
200 163 0.49
201 164 0.50
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (199 bp):
TTGGTATACTTCTTTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCAATCTGCTTCTCTG
TCCTTATCAGGAAGAAGAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATT
GCTTCACCTGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGCTCGCATTGAGCCC
TGAG
Found at i:2047 original size:158 final size:157
Alignment explanation
Indices: 1857--2171 Score: 603
Period size: 158 Copynumber: 2.0 Consensus size: 157
1847 CCGCCTAACT
1857 TGTTTCAATCTGCTTCTCTGTACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCAT
1 TGTTTCAATCTGCTTCTCTGTACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCAT
*
1922 CAGGAAGCTAACCTTTTTATTGCTTCACCTTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTCG
66 CAGGAAGCTAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTCG
1987 AAGATTTGTTGGCATTGAGTTGGTATA
131 AAGATTTGTTGGCATTGAGTTGGTATA
2014 NTGTTTCAATCTGCTTCTCTGTACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCA
1 -TGTTTCAATCTGCTTCTCTGTACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCA
*
2079 TCAGGAAGCTAACCTTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTC
65 TCAGGAAGCTAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTC
2144 GAAGATTTGTTGGCATTGAGTTGGTATA
130 GAAGATTTGTTGGCATTGAGTTGGTATA
2172 CTTCTTTGTA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 155 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (157 bp):
TGTTTCAATCTGCTTCTCTGTACTTTATCAGGAAGAAAAATTTGGTTCACTTCTCAGTGTCTCAT
CAGGAAGCTAACCTTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAAGAAGCTTGGGTTCG
AAGATTTGTTGGCATTGAGTTGGTATA
Found at i:2633 original size:50 final size:51
Alignment explanation
Indices: 2564--2705 Score: 141
Period size: 50 Copynumber: 2.8 Consensus size: 51
2554 CTCGTCATGT
*
2564 TTCTAAGGTAC-CGAGTTCGCCATTGCGACTTAAACCTTTCCCCTTTAAGTC
1 TTCTGAGGTACACG-GTTCGCCATTGCGACTTAAACCTTTCCCCTTTAAGTC
* * * * **
2615 TTC-GTGGTAC-TGGATTCGCCGTTGC-AGCTTAAATCTTT-CCCTTTTTGTC
1 TTCTGAGGTACACGG-TTCGCCATTGCGA-CTTAAACCTTTCCCCTTTAAGTC
* *
2664 TTCTGAGGTACACGGTCCTCCATTGCGACTTAAACCTTTCCC
1 TTCTGAGGTACACGGTTCGCCATTGCGACTTAAACCTTTCCC
2706 TTTTGTATCT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
49 14 0.19
50 50 0.69
51 8 0.11
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.36
Consensus pattern (51 bp):
TTCTGAGGTACACGGTTCGCCATTGCGACTTAAACCTTTCCCCTTTAAGTC
Found at i:2722 original size:100 final size:101
Alignment explanation
Indices: 2558--2767 Score: 248
Period size: 100 Copynumber: 2.1 Consensus size: 101
2548 ACCTTTCTCG
* * *
2558 TCATGT-TTCTAAGGTAC-CGAGTTCGCCATTGCGACTTAAACCTTTCCCCTTTAAGTCTTCGTG
1 TCATGTCTTCTGAGGTACACG-GTCCTCCATTGCGACTTAAACCTTTCCCCTTTAAGTCTTCGTG
* *
2621 GTACTGGATTCGCCGTTGCAG-CTTAAATCTTTCCCT
65 GTACTGAATCCGCCGTTGCAGTCTTAAATCTTTCCCT
** * * *
2657 TTTTGTCTTCTGAGGTACACGGTCCTCCATTGCGACTTAAACCTTTCCCTTTTGTA-TCTTTGTG
1 TCATGTCTTCTGAGGTACACGGTCCTCCATTGCGACTTAAACCTTTCCCCTTT-AAGTCTTCGTG
* * * *
2721 GTTCTGAATCCGCCGTTGCGGTTTTAGATCTTTCCCT
65 GTACTGAATCCGCCGTTGCAGTCTTAAATCTTTCCCT
2758 TCATGTCTTC
1 TCATGTCTTC
2768 ATGGTATTGA
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
99 4 0.04
100 63 0.69
101 24 0.26
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (101 bp):
TCATGTCTTCTGAGGTACACGGTCCTCCATTGCGACTTAAACCTTTCCCCTTTAAGTCTTCGTGG
TACTGAATCCGCCGTTGCAGTCTTAAATCTTTCCCT
Found at i:2740 original size:50 final size:48
Alignment explanation
Indices: 2581--2740 Score: 133
Period size: 50 Copynumber: 3.2 Consensus size: 48
2571 GTACCGAGTT
* * * *
2581 CGCCATTGCGACTTAAACCTTTCCCCTTTAAGTCTTCGTGGTACTGGATT
1 CGCCATTGCGACTTAAACCTTTCCCTTTTTA-TCTTTGTGGTACT-GATC
* * * * * *
2631 CGCCGTTGC-AGCTTAAATCTTTCCCTTTTTGTCTTCTGAGGTACACGGTC
1 CGCCATTGCGA-CTTAAACCTTTCCCTTTTTATCTT-TGTGGTAC-TGATC
* *
2681 CTCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTTCTGAATC
1 CGCCATTGCGACTTAAACCTTTCCCTTTT-TATCTTTGTGGTACTG-ATC
*
2731 CGCCGTTGCG
1 CGCCATTGCG
2741 GTTTTAGATC
Statistics
Matches: 84, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
49 6 0.07
50 72 0.86
51 6 0.07
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.38
Consensus pattern (48 bp):
CGCCATTGCGACTTAAACCTTTCCCTTTTTATCTTTGTGGTACTGATC
Found at i:6358 original size:36 final size:35
Alignment explanation
Indices: 6318--6388 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
6308 AGAAGAAGGA
6318 ATGACCTGCCGTATTGTCTATCAGGGTATCGATAT
1 ATGACCTGCCGTATTGTCTATCAGGGTATCGATAT
*
6353 NATGACCTGCTGTATTGTCTATCAGGGTATCGATAT
1 -ATGACCTGCCGTATTGTCTATCAGGGTATCGATAT
6389 GAGGCAGCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (35 bp):
ATGACCTGCCGTATTGTCTATCAGGGTATCGATAT
Done.