Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001437.1 Kokia drynarioides strain JFW-HI SEQ_112946, 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: 53922
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:1140 original size:30 final size:28
Alignment explanation
Indices: 1104--1596 Score: 403
Period size: 29 Copynumber: 16.8 Consensus size: 28
1094 GGAGTCCCTA
1104 AACCTTCCAAAAATCTCATTTTTAACCCCG
1 AACCTTCCAAAAATCTCA-TTTT-ACCCCG
* *
1134 AACCTTCCAAAAATTATCATTTTACCCCT
1 AACCTTCCAAAAA-TCTCATTTTACCCCG
* *
1163 AAACTTTCAAAAAT-TCCATTTTGACCCCG
1 AACCTTCCAAAAATCT-CATTTT-ACCCCG
**
1192 AACCTTCCAAAAAT-TACCATTTTACCCTT
1 AACCTTCCAAAAATCT--CATTTTACCCCG
* *
1221 AAACTTCCAAAAATCTCATTTTTAACCCCA
1 AACCTTCCAAAAATCTCA-TTTT-ACCCCG
* *
1251 AACCTTCCAAAAATCCCATTTTTAACCCCA
1 AACCTTCCAAAAATCTCA-TTTT-ACCCCG
* *
1281 AACCTTCC-AAAATCACTATTTTACCCTCA
1 AACCTTCCAAAAATCTC-ATTTTACCC-CG
*
1310 AACCTTCCAAAAAT-TACCATTTTACCCCT
1 AACCTTCCAAAAATCT--CATTTTACCCCG
* * *
1339 AAACTTCCAAAAATCCCATTTTAAACACCG
1 AACCTTCCAAAAATCTCATTTT--ACCCCG
* *
1369 AACCTTCCAAAAATCACCATTTTAAACCTCG
1 AACCTTCCAAAAATC-TCATTTT--ACCCCG
*
1400 AACCTTCCAAAAATCACCATTTTACCCTCG
1 AACCTTCCAAAAATC-TCATTTTACCC-CG
1430 AACCTTCCAAAAAT-TACCATTTTACCCCG
1 AACCTTCCAAAAATCT--CATTTTACCCCG
1459 AA-CTTCCAAAAATCTCATTTTTAACCCCG
1 AACCTTCCAAAAATCTCA-TTTT-ACCCCG
*
1488 AACCTTCCAAAAGT-TACCATTTTACCCTCG
1 AACCTTCCAAAAATCT--CATTTTACCC-CG
*
1518 AAAC-TCCAAAAATC-CAATTTTAACCCCG
1 AACCTTCCAAAAATCTC-ATTTT-ACCCCG
*
1546 AACCTTCCAAAAAT-TACCATTTTACCCCC
1 AACCTTCCAAAAATCT--CATTTTACCCCG
* *
1575 AAACTTCCAAAAATCCCATTTT
1 AACCTTCCAAAAATCTCATTTT
1597 CGACCTCGAA
Statistics
Matches: 396, Mismatches: 33, Indels: 70
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.01
28 50 0.13
29 150 0.38
30 148 0.37
31 44 0.11
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (28 bp):
AACCTTCCAAAAATCTCATTTTACCCCG
Found at i:1618 original size:58 final size:58
Alignment explanation
Indices: 1107--1596 Score: 596
Period size: 58 Copynumber: 8.3 Consensus size: 58
1097 GTCCCTAAAC
* * *
1107 CTTCCAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTATCATTTTACCCCTAAA
1 CTTCCAAAAATCCCA-TTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAA
* * * **
1166 CTTTCAAAAATTCCATTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCTTAAA
1 CTTCCAAAAATCCCATTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAA
* * * *
1224 CTTCCAAAAATCTCATTTTTAACCCCAAACCTTCCAAAAA-TCCCATTTTTAACCCCAAA
1 CTTCCAAAAATCCCA-TTTTAACCCCGAACCTTCCAAAAATTACCA-TTTTACCCCCAAA
* * *
1283 CCTTCC-AAAATCACTATTTT-ACCCTCAAACCTTCCAAAAATTACCATTTTACCCCTAAA
1 -CTTCCAAAAATC-CCATTTTAACCC-CGAACCTTCCAAAAATTACCATTTTACCCCCAAA
* * * * *
1342 CTTCCAAAAATCCCATTTTAAACACCGAACCTTCCAAAAATCACCATTTTAAACCTCGAAC
1 CTTCCAAAAATCCCATTTT-AACCCCGAACCTTCCAAAAATTACCATTTT--ACCCCCAAA
*
1403 CTTCCAAAAATCACCATTTT-ACCCTCGAACCTTCCAAAAATTACCATTTTA-CCCCGAA
1 CTTCCAAAAATC-CCATTTTAACCC-CGAACCTTCCAAAAATTACCATTTTACCCCCAAA
* * *
1461 CTTCCAAAAATCTCATTTTTAACCCCGAACCTTCCAAAAGTTACCATTTTACCCTCGAAA
1 CTTCCAAAAATCCCA-TTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCC-CCAAA
*
1521 C-TCCAAAAATCCAATTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAA
1 CTTCCAAAAATCCCATTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAA
1578 CTTCCAAAAATCCCATTTT
1 CTTCCAAAAATCCCATTTT
1597 CGACCTCGAA
Statistics
Matches: 371, Mismatches: 42, Indels: 37
0.82 0.09 0.08
Matches are distributed among these distances:
57 7 0.02
58 168 0.45
59 127 0.34
60 20 0.05
61 42 0.11
62 7 0.02
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (58 bp):
CTTCCAAAAATCCCATTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAA
Found at i:2880 original size:41 final size:41
Alignment explanation
Indices: 2835--2965 Score: 181
Period size: 41 Copynumber: 3.2 Consensus size: 41
2825 TAAATAAATT
* ***
2835 ACCTTTAGCGGCGCTTTTTAATAAACGCCGCTAATGCTCTG
1 ACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
* **
2876 ACCTTTAGCGATGCTTTCCCATAAACGCCTTTAATGCTCTG
1 ACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
* *
2917 ACCTTTAGCAGTGCTTTCCCATAAACGCCGCTAATACTCTG
1 ACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
2958 ACCTTTAG
1 ACCTTTAG
2966 TGGCACTAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (41 bp):
ACCTTTAGCGGTGCTTTCCCATAAACGCCGCTAATGCTCTG
Found at i:2979 original size:24 final size:24
Alignment explanation
Indices: 2947--2996 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2937 ATAAACGCCG
*
2947 CTAATACTCTGACCTTTAGTGGCA
1 CTAATACTCTGACCTTTAGCGGCA
2971 CTAATACTCTGACCTTTAGCGGCA
1 CTAATACTCTGACCTTTAGCGGCA
2995 CT
1 CT
2997 TTCTCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (24 bp):
CTAATACTCTGACCTTTAGCGGCA
Found at i:6321 original size:20 final size:18
Alignment explanation
Indices: 6298--6340 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
6288 AGAAAATTAG
6298 TTATAAAAATTTCAAAATAT
1 TTATAAAAATTT-AAAAT-T
*
6318 TTATGAAAATTTAAAATT
1 TTATAAAAATTTAAAATT
6336 TTATA
1 TTATA
6341 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTATAAAAATTTAAAATT
Found at i:6347 original size:17 final size:18
Alignment explanation
Indices: 6327--6369 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6317 TTTATGAAAA
*
6327 TTTAAAATT-TTATATTT
1 TTTAAAATTATAATATTT
*
6344 TTTAAAAATTATAATTTTT
1 TTT-AAAATTATAATATTT
6363 TTTAAAA
1 TTTAAAA
6370 AAAACTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 10 0.45
19 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAAATTATAATATTT
Found at i:6350 original size:24 final size:24
Alignment explanation
Indices: 6314--6361 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6304 AAATTTCAAA
*
6314 ATATTTATGAAAATTTAAAATTTT
1 ATATTTATGAAAAATTAAAATTTT
* * *
6338 ATATTTTTTAAAAATTATAATTTT
1 ATATTTATGAAAAATTAAAATTTT
6362 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATTTATGAAAAATTAAAATTTT
Found at i:8015 original size:27 final size:28
Alignment explanation
Indices: 7949--8020 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
7939 TTTTTAAAAT
* * **
7949 TAAAAAATGTATA-ATTTTTAAAAATTT
1 TAAAAAATATATATAATTTTAAAAATCA
* *
7976 TTAAGAATATATATAATTTTAAAAATCA
1 TAAAAAATATATATAATTTTAAAAATCA
8004 TAAAAAATTATATATAA
1 TAAAAAA-TATATATAA
8021 AATGAAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 10 0.29
28 16 0.46
29 9 0.26
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (28 bp):
TAAAAAATATATATAATTTTAAAAATCA
Found at i:8826 original size:11 final size:11
Alignment explanation
Indices: 8810--8835 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8800 TTTATTAATT
8810 AAAATTAAAAC
1 AAAATTAAAAC
8821 AAAATTAAAAC
1 AAAATTAAAAC
8832 AAAA
1 AAAA
8836 AATACAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATTAAAAC
Found at i:22827 original size:43 final size:43
Alignment explanation
Indices: 22779--22998 Score: 189
Period size: 43 Copynumber: 5.2 Consensus size: 43
22769 TGTACATGCT
* * * *
22779 TTACTTTGGTTTATCCAATGATGCATTCTATGTGCGAGTATAA
1 TTACTTTGGTATATCCAATGATGCACTCTGTGTGCCAGTATAA
* * *** * *
22822 TTACTTCGGCATATTTGATGATGCA--CTGTGTGCTAGTATAG
1 TTACTTTGGTATATCCAATGATGCACTCTGTGTGCCAGTATAA
* * * * *
22863 TTTCTTTGGTATATCCAATGATGCATTGTGTGTGTCTGTATAA
1 TTACTTTGGTATATCCAATGATGCACTCTGTGTGCCAGTATAA
* **
22906 TTACTTTGGTATATCCAAT-ATGCACT-TATGTGCCAACATAA
1 TTACTTTGGTATATCCAATGATGCACTCTGTGTGCCAGTATAA
* * *
22947 TTACTTTGGTTTA-CTAAATGATGCACTATGTGTGCCAGTATAA
1 TTACTTTGGTATATC-CAATGATGCACTCTGTGTGCCAGTATAA
*
22990 TTGCTTTGG
1 TTACTTTGG
22999 CTTGTCTGAT
Statistics
Matches: 139, Mismatches: 33, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 57 0.41
42 13 0.09
43 68 0.49
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (43 bp):
TTACTTTGGTATATCCAATGATGCACTCTGTGTGCCAGTATAA
Found at i:22954 original size:84 final size:83
Alignment explanation
Indices: 22779--22999 Score: 212
Period size: 84 Copynumber: 2.6 Consensus size: 83
22769 TGTACATGCT
* * * ***
22779 TTACTTTGGTTTATCCAATGATGCATTCTATGTGCGAGTATAATTACTTCGGCATATTTGATGAT
1 TTACTTTGGTTTATCCAATGATGCATTATGTGTGC-AGTATAATTACTTTGGCATATCCAATGAT
* * ** *
22844 GCACTGTGTGCTAGTATAG
65 GCACTATGTGCCAACATAA
* * * * *
22863 TTTCTTTGGTATATCCAATGATGCATTGTGTGTGTCTGTATAATTACTTTGGTATATCCAAT-AT
1 TTACTTTGGTTTATCCAATGATGCATTATGTGTG-CAGTATAATTACTTTGGCATATCCAATGAT
22927 GCACTTATGTGCCAACATAA
65 GCAC-TATGTGCCAACATAA
* * *
22947 TTACTTTGGTTTA-CTAAATGATGCACTATGTGTGCCAGTATAATTGCTTTGGC
1 TTACTTTGGTTTATC-CAATGATGCATTATGTGTG-CAGTATAATTACTTTGGC
23000 TTGTCTGATT
Statistics
Matches: 110, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
83 7 0.06
84 102 0.93
85 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.41
Consensus pattern (83 bp):
TTACTTTGGTTTATCCAATGATGCATTATGTGTGCAGTATAATTACTTTGGCATATCCAATGATG
CACTATGTGCCAACATAA
Found at i:43833 original size:19 final size:20
Alignment explanation
Indices: 43809--43865 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
43799 AAAATTTTAA
*
43809 AATTTTTATAAAT-ATTTTC
1 AATTTTTAAAAATCATTTTC
43828 AA-TTTTAAAAATCATTTTC
1 AATTTTTAAAAATCATTTTC
* *
43847 AATTTTTGAAAATTATTTT
1 AATTTTTAAAAATCATTTT
43866 GATTATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.27
19 10 0.30
20 14 0.42
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTTTTAAAAATCATTTTC
Found at i:43858 original size:20 final size:18
Alignment explanation
Indices: 43809--43865 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
43799 AAAATTTTAA
43809 AATTTTTATAAATATTTTC
1 AATTTTTA-AAATATTTTC
*
43828 AATTTTAAAAATCATTTTC
1 AATTTTTAAAAT-ATTTTC
43847 AATTTTTGAAAATTATTTT
1 AATTTTT-AAAA-TATTTT
43866 GATTATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 4 0.12
19 19 0.58
20 9 0.27
21 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTTTAAAATATTTTC
Found at i:48221 original size:18 final size:18
Alignment explanation
Indices: 48198--48233 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
48188 CCATTTTGTG
48198 AAAGAATCTCGTTAAAAT
1 AAAGAATCTCGTTAAAAT
48216 AAAGAATCTCGTTAAAAT
1 AAAGAATCTCGTTAAAAT
48234 CACCTATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAGAATCTCGTTAAAAT
Found at i:53304 original size:17 final size:17
Alignment explanation
Indices: 53280--53353 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
53270 TTGGAAATTG
53280 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
53297 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
53314 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
53331 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
53348 AATTTA
1 AATTTA
53354 GAAAAGTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.