Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015063.1 Kokia drynarioides strain JFW-HI SEQ_130107, 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: 43438
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:5208 original size:98 final size:98
Alignment explanation
Indices: 5020--5210 Score: 255
Period size: 98 Copynumber: 1.9 Consensus size: 98
5010 TCTTTACGAA
*
5020 AAGGATATTTGATTATCTCGATTTGAAGAAAAAAATTGCACCTAGTGAGTTAAGACGCAATATTT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAAATTGCACCTAGTGAGTTAAGACGCAATATTT
** * *
5085 CGGAATCGAAGATAAGGAAACATTGCCTCAATT
66 CAAAACCGAAGATAAAGAAACATTGCCTCAATT
*
5118 AAGGATATTCGATTATTTCGATTTGAAGAAAAAAATTGCACCTAGTGAGTTAATG-CGCAA-ATT
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAAAATTGCACCTAGTGAGTTAA-GACGCAATA-T
*
5181 TTCAAAACCCGAA-ATGAAAG-AATATTGCCT
64 TTCAAAA-CCGAAGAT-AAAGAAACATTGCCT
5211 TGATATTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
97 1 0.01
98 73 0.89
99 8 0.10
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (98 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAAAATTGCACCTAGTGAGTTAAGACGCAATATTT
CAAAACCGAAGATAAAGAAACATTGCCTCAATT
Found at i:5530 original size:30 final size:30
Alignment explanation
Indices: 5488--5641 Score: 148
Period size: 30 Copynumber: 5.1 Consensus size: 30
5478 CTTGAGGGTG
* * *
5488 AAATGGTAATTTTAGGAAAATTCAGGGTTAA
1 AAATGG-AATTTTTGGAAATTTCGGGGTTAA
* *
5519 AAATGGAATTTTTGGAAGTTTGGGGGTTAA
1 AAATGGAATTTTTGGAAATTTCGGGGTTAA
* * * *
5549 AAATGGGATTTTTTGAAGTTTTGGGGTTAA
1 AAATGGAATTTTTGGAAATTTCGGGGTTAA
*** *
5579 AAATGGAATTTTTGGAAATTTTTTGGTAAA
1 AAATGGAATTTTTGGAAATTTCGGGGTTAA
* * *
5609 AAATGGGATTTTTGG-AAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAATTTCGGGGTTAA
5638 AAAT
1 AAAT
5642 AAGATTTTTG
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
29 12 0.12
30 84 0.82
31 6 0.06
ACGTcount: A:0.34, C:0.01, G:0.28, T:0.37
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAATTTCGGGGTTAA
Found at i:5578 original size:60 final size:59
Alignment explanation
Indices: 5512--5659 Score: 181
Period size: 60 Copynumber: 2.5 Consensus size: 59
5502 GGAAAATTCA
* * *
5512 GGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTTAAAAATGGGATTTTTTGAAGTTTTG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAAATGGGATTTTTGGAAG-TTCG
* ***
5572 GGGTTAAAAATGGAATTTTTGGAAATTTTTTGGTAAAAAATGGGATTTTTGGAAGTTCG
1 GGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAAATGGGATTTTTGGAAGTTCG
* *
5631 GGGGTAAAAAT-AAGATTTTTGGATAGTTT
1 GGGTTAAAAATGGA-ATTTTTGGA-AGTTT
5660 AGGGACCTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
58 1 0.01
59 22 0.29
60 53 0.70
ACGTcount: A:0.31, C:0.01, G:0.29, T:0.39
Consensus pattern (59 bp):
GGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAAATGGGATTTTTGGAAGTTCG
Found at i:5596 original size:90 final size:91
Alignment explanation
Indices: 5488--5659 Score: 222
Period size: 90 Copynumber: 1.9 Consensus size: 91
5478 CTTGAGGGTG
* *
5488 AAATGGTAATTTTAGGAAAATTCAGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTTAAAAAT
1 AAATGGTAATTTTAGGAAAATTCAGGGTAAAAAATGGAATTTTTGGAAGTTCGGGGG-TAAAAAT
** *
5553 GGGATTTTTTGA-AGTTTTGGGGTTAA
65 AAGATTTTTGGATAGTTTTGGGGTTAA
* * *** *
5579 AAATGG-AATTTTTGGAAATTTTTTGGTAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATA
1 AAATGGTAATTTTAGGAAAATTCAGGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATA
5643 AGATTTTTGGATAGTTT
66 AGATTTTTGGATAGTTT
5660 AGGGACCTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
89 16 0.23
90 47 0.68
91 6 0.09
ACGTcount: A:0.33, C:0.01, G:0.27, T:0.38
Consensus pattern (91 bp):
AAATGGTAATTTTAGGAAAATTCAGGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATA
AGATTTTTGGATAGTTTTGGGGTTAA
Found at i:5647 original size:29 final size:29
Alignment explanation
Indices: 5516--5659 Score: 153
Period size: 30 Copynumber: 4.8 Consensus size: 29
5506 AATTCAGGGT
*
5516 TAAAAATGGAATTTTTGGAAGTTTGGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* *
5545 TTAAAAATGGGATTTTTTGAAGTTTTGGGGT
1 -TAAAAATGGGATTTTTGGAAG-TTTGGGGG
* * ***
5576 TAAAAATGGAATTTTTGGAAATTTTTTGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
*
5605 TAAAAAATGGGATTTTTGGAAGTTCGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGGGGG
**
5635 TAAAAATAAGATTTTTGGATAGTTT
1 TAAAAATGGGATTTTTGGA-AGTTT
5660 AGGGACCTTC
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
29 21 0.23
30 64 0.70
31 7 0.08
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.40
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTGGGGG
Found at i:6269 original size:17 final size:17
Alignment explanation
Indices: 6247--6280 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6237 NNAATTTTAG
6247 TTTAAAATAAACTCAAA
1 TTTAAAATAAACTCAAA
* *
6264 TTTAAATTAAATTCAAA
1 TTTAAAATAAACTCAAA
6281 CTCATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTAAAATAAACTCAAA
Found at i:15320 original size:25 final size:25
Alignment explanation
Indices: 15267--15314 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
15257 CGAAGAAACG
*
15267 AACAGTCGAAATTCAAACAAATTTA
1 AACAGTCGAAACTCAAACAAATTTA
15292 AACAGTCGATAACT-AAA-AAATTT
1 AACAGTCGA-AACTCAAACAAATTT
15315 CCAACATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 12 0.57
26 3 0.14
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (25 bp):
AACAGTCGAAACTCAAACAAATTTA
Found at i:16287 original size:17 final size:17
Alignment explanation
Indices: 16267--16305 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
16257 TATAATCTAA
*
16267 TTTTTATTAATTGTGTT
1 TTTTTATTAATTGTCTT
* *
16284 TTTTTTTTAATTTTCTT
1 TTTTTATTAATTGTCTT
16301 TTTTT
1 TTTTT
16306 CCGTAGTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTATTAATTGTCTT
Found at i:19730 original size:104 final size:104
Alignment explanation
Indices: 19546--19754 Score: 382
Period size: 104 Copynumber: 2.0 Consensus size: 104
19536 TTTAGGACTC
*
19546 TAATATTCATTAAAAATAGAGTTTTATTTCATTTATATTTCCTATATCTATAAATATAGATTTTA
1 TAATATTCATTAAAAATAGAATTTTATTTCATTTATATTTCCTATATCTATAAATATAGATTTTA
19611 AAAAAACATTATAAATATCCCTAAAATTCAGAGTTGTTT
66 AAAAAACATTATAAATATCCCTAAAATTCAGAGTTGTTT
*
19650 TAATATTCATTAAAAATATAATTTTATTTCATTTATATTTCCTATATCTATAAATATAGATTTTA
1 TAATATTCATTAAAAATAGAATTTTATTTCATTTATATTTCCTATATCTATAAATATAGATTTTA
* *
19715 AATAAACATTGTAAATATCCCTAAAATTCAGAGTTGTTT
66 AAAAAACATTATAAATATCCCTAAAATTCAGAGTTGTTT
19754 T
1 T
19755 GCTTTTTCTA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (104 bp):
TAATATTCATTAAAAATAGAATTTTATTTCATTTATATTTCCTATATCTATAAATATAGATTTTA
AAAAAACATTATAAATATCCCTAAAATTCAGAGTTGTTT
Found at i:27524 original size:24 final size:24
Alignment explanation
Indices: 27496--27546 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27486 AGAAATAATC
* * *
27496 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTATATTTAGTTG
*
27520 TTTCAATTAAACTATGTTTAGTTG
1 TTTCAATTAAACTATATTTAGTTG
27544 TTT
1 TTT
27547 GAGTCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTATATTTAGTTG
Found at i:29551 original size:24 final size:24
Alignment explanation
Indices: 29486--29560 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
29476 AGAAATATTC
* * *
29486 TTTCAGTTAAACTCTGCTTATTTA
1 TTTCAATTAAACTCTGTTTATTTG
*
29510 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
29534 TTTCAATTAAGCTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
29558 TTT
1 TTT
29561 GAGTCAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:31618 original size:95 final size:95
Alignment explanation
Indices: 31455--31667 Score: 426
Period size: 95 Copynumber: 2.2 Consensus size: 95
31445 ATAGCTACTT
31455 GCCATAGCATTTAAACTTGCCAATGAGATAGAATTAGCCTAATCACAACTTGAAATAGCTACTTG
1 GCCATAGCATTTAAACTTGCCAATGAGATAGAATTAGCCTAATCACAACTTGAAATAGCTACTTG
31520 CCGAAAATTTGAGTGGCTGAAGCCGAAGCA
66 CCGAAAATTTGAGTGGCTGAAGCCGAAGCA
31550 GCCATAGCATTTAAACTTGCCAATGAGATAGAATTAGCCTAATCACAACTTGAAATAGCTACTTG
1 GCCATAGCATTTAAACTTGCCAATGAGATAGAATTAGCCTAATCACAACTTGAAATAGCTACTTG
31615 CCGAAAATTTGAGTGGCTGAAGCCGAAGCA
66 CCGAAAATTTGAGTGGCTGAAGCCGAAGCA
31645 GCCATAGCATTTAAACTTGCCAA
1 GCCATAGCATTTAAACTTGCCAA
31668 GTTATGTAAA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 118 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (95 bp):
GCCATAGCATTTAAACTTGCCAATGAGATAGAATTAGCCTAATCACAACTTGAAATAGCTACTTG
CCGAAAATTTGAGTGGCTGAAGCCGAAGCA
Found at i:31920 original size:9 final size:9
Alignment explanation
Indices: 31906--31969 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
31896 TAATGTTCAC
31906 TTAACCGAA
1 TTAACCGAA
31915 TTAACC-AA
1 TTAACCGAA
31923 TTCAA---AA
1 TT-AACCGAA
31930 TTAACCGAA
1 TTAACCGAA
*
31939 TTAACCAAAA
1 TTAACC-GAA
*
31949 GTAACCGAAA
1 TTAACCG-AA
31959 TTAACCGAA
1 TTAACCGAA
31968 TT
1 TT
31970 GGTAATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 2 0.04
7 4 0.09
8 4 0.09
9 20 0.44
10 15 0.33
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.23
Consensus pattern (9 bp):
TTAACCGAA
Found at i:31953 original size:19 final size:20
Alignment explanation
Indices: 31925--31964 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
31915 TTAACCAATT
*
31925 CAAAATTAACCG-AATTAAC
1 CAAAAGTAACCGAAATTAAC
31944 CAAAAGTAACCGAAATTAAC
1 CAAAAGTAACCGAAATTAAC
31964 C
1 C
31965 GAATTGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (20 bp):
CAAAAGTAACCGAAATTAAC
Found at i:31963 original size:10 final size:10
Alignment explanation
Indices: 31927--31967 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
31917 AACCAATTCA
31927 AAATTAACCG
1 AAATTAACCG
*
31937 -AATTAACCA
1 AAATTAACCG
*
31946 AAAGTAACCG
1 AAATTAACCG
31956 AAATTAACCG
1 AAATTAACCG
31966 AA
1 AA
31968 TTGGTAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.17
Consensus pattern (10 bp):
AAATTAACCG
Found at i:33053 original size:22 final size:22
Alignment explanation
Indices: 33028--33077 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
33018 ATGTTTAATA
33028 ATATTTAGCATTGTAATATTT-G
1 ATATTTA-CATTGTAATATTTAG
* * *
33050 ATATTGACATTTTAATTTTTAG
1 ATATTTACATTGTAATATTTAG
33072 ATATTT
1 ATATTT
33078 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (22 bp):
ATATTTACATTGTAATATTTAG
Found at i:33065 original size:21 final size:22
Alignment explanation
Indices: 33036--33076 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
33026 TAATATTTAG
33036 CATTGTAATATTT-GATATTGA
1 CATTGTAATATTTAGATATTGA
* *
33057 CATTTTAATTTTTAGATATT
1 CATTGTAATATTTAGATATT
33077 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (22 bp):
CATTGTAATATTTAGATATTGA
Done.