Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000206.1 Kokia drynarioides strain JFW-HI SEQ_110900, 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: 6615
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1844 original size:27 final size:28
Alignment explanation
Indices: 1784--1844 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1774 AGGGTTTAAG
* * *
1784 TGTTACCGATTAAGCACTACTAGTCAGA
1 TGTTACCAATCAAGCACTACTAGTCAAA
* *
1812 GGTTACCAATCAAGCACTAC-CGTCAAA
1 TGTTACCAATCAAGCACTACTAGTCAAA
1839 TGTTAC
1 TGTTAC
1845 ATATTTAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (28 bp):
TGTTACCAATCAAGCACTACTAGTCAAA
Found at i:2033 original size:47 final size:47
Alignment explanation
Indices: 1982--2228 Score: 201
Period size: 47 Copynumber: 5.4 Consensus size: 47
1972 CGGCTTATGA
* * * **
1982 TTTAGGGTTTAGTGTTTAAAGCTTGATCAAACTTTATCGATTTAAGG
1 TTTAGGGTTTAATGTTTAAAGTTTGATTAGGCTTTATCGATTTAAGG
* * *
2029 TTTAGTGTTTAATGCTTAAGGTTT-AGTTAGGCTTTATC----T-A--
1 TTTAGGGTTTAATGTTTAAAGTTTGA-TTAGGCTTTATCGATTTAAGG
* * *
2069 TTTAGGGTTT-ATGGTTTAAAGTTTGATTGGGCTTTATCAATTTAGGG
1 TTTAGGGTTTAAT-GTTTAAAGTTTGATTAGGCTTTATCGATTTAAGG
* * *
2116 TTTAAGGTTTAATGTTT-AGGATTT-ACTTAGGCTTTATCAATTTAAGG
1 TTTAGGGTTTAATGTTTAAAG-TTTGA-TTAGGCTTTATCGATTTAAGG
* * * * *
2163 TTTAGAGTTTAGTGCTTAGAGTTTGATCAGGCTTTATCGATTTAAGG
1 TTTAGGGTTTAATGTTTAAAGTTTGATTAGGCTTTATCGATTTAAGG
*
2210 TTTATGGTTTAATGTTTAA
1 TTTAGGGTTTAATGTTTAA
2229 GGTTCACTCA
Statistics
Matches: 155, Mismatches: 30, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
39 2 0.01
40 29 0.19
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 4 0.03
47 112 0.72
48 4 0.03
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (47 bp):
TTTAGGGTTTAATGTTTAAAGTTTGATTAGGCTTTATCGATTTAAGG
Found at i:2073 original size:40 final size:41
Alignment explanation
Indices: 2029--2166 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 41
2019 CGATTTAAGG
* * * *
2029 TTTAGTGTTTAATGCTTAAGGTTTAG-TTAGGCTTTATCTA
1 TTTAGGGTTTAATGTTTAAAGTTTAGATTAGGCTTTATCAA
*
2069 TTTAGGGTTT-ATGGTTTAAAGTTT-GATTGGGCTTTATCAA
1 TTTAGGGTTTAAT-GTTTAAAGTTTAGATTAGGCTTTATCAA
* *
2109 TTTAGGGTTTAAGGTTTAATGTTTAGGATTTACTTAGGCTTTATCAA
1 TTTAGGGTTTAATGTTTAAAGTTTA-G----A-TTAGGCTTTATCAA
*
2156 TTTAAGGTTTA
1 TTTAGGGTTTA
2167 GAGTTTAGTG
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
39 3 0.04
40 50 0.63
41 1 0.01
42 1 0.01
46 1 0.01
47 23 0.29
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.49
Consensus pattern (41 bp):
TTTAGGGTTTAATGTTTAAAGTTTAGATTAGGCTTTATCAA
Found at i:2076 original size:87 final size:88
Alignment explanation
Indices: 1981--2267 Score: 264
Period size: 87 Copynumber: 3.2 Consensus size: 88
1971 TCGGCTTATG
* **
1981 ATTTAGGGTTTAGTGTTTAAAGCTTGATCAAACTTTATCGATTTAAGGTTTAGTGTTTAATGCTT
1 ATTTAGGGTTTAGTGTTTAAAGTTTGATCAGGCTTTATCGATTTAAGGTTTAGTGTTTAATG-TT
*
2046 AAGGTTTAGTTAGGCTTTATC-T-
65 AAGGTTTACTTAGGCTTTATCATA
** * *
2068 ATTTAGGGTTTA-TGGTTTAAAGTTTGATTGGGCTTTATCAATTTAGGGTTTAAG-GTTTAATGT
1 ATTTAGGGTTTAGT-GTTTAAAGTTTGATCAGGCTTTATCGATTTAAGGTTT-AGTGTTTAATGT
*
2131 TTAGGATTTACTTAGGCTTTATCAATTTA
64 TAAGG-TTTACTTAGGCTTTATC-A--TA
* * *
2160 AGGTTTAGAGTTTAGTGCTTAGAGTTTGATCAGGCTTTATCGATTTAAGGTTTA-TGGTTTAATG
1 A--TTTAGGGTTTAGTGTTTAAAGTTTGATCAGGCTTTATCGATTTAAGGTTTAGT-GTTTAATG
* * * *
2224 TTTAAGGTTCACTCAGG-TTGAAC-TA
63 -TTAAGGTTTACTTAGGCTTTATCATA
* *
2249 ATTTAGGGTTGAGGGTTTA
1 ATTTAGGGTTTAGTGTTTA
2268 GCACTTGGGA
Statistics
Matches: 161, Mismatches: 25, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
86 6 0.04
87 80 0.50
88 2 0.01
89 3 0.02
91 1 0.01
92 1 0.01
93 5 0.03
94 57 0.35
95 6 0.04
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (88 bp):
ATTTAGGGTTTAGTGTTTAAAGTTTGATCAGGCTTTATCGATTTAAGGTTTAGTGTTTAATGTTA
AGGTTTACTTAGGCTTTATCATA
Found at i:2302 original size:47 final size:47
Alignment explanation
Indices: 2098--2446 Score: 229
Period size: 47 Copynumber: 7.4 Consensus size: 47
2088 AGTTTGATTG
** * * * * * *
2098 GGCTTTATCAATTTAGGGTTTAAGGTTTAATGTTTAGGATTTACTTA
1 GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTTAGGATTCAATTA
** * * * ** *
2145 GGCTTTATCAATTTAAGGTTTAGAGTTTAGTGCTTA-GAGTTTGATCA
1 GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTTAGGA-TTCAATTA
* * * * * * * *
2192 GGCTTTATCGATTTAAGGTTTATGGTTTAATGTTTAAGG-TTCACTCA
1 GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTT-AGGATTCAATTA
* * * ** *
2239 GG-TTGAACTAATTTAGGGTTGAGGGTTTAGCACTTGGGATTCAATTA
1 GGCTT-TATTGATTTAGGGTTGAGGGTTTAGTGCTTAGGATTCAATTA
* * *
2286 GGCTTTCTTGATTTAGGGTTGAGGGTTTAGTGCTTAAGG-TTCAGTCA
1 GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTT-AGGATTCAATTA
* * * *
2333 AGCTTTATTGATTTAGGATTGAGGGTTTAGTGTTTAGGATTCAATTG
1 GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTTAGGATTCAATTA
* * * * * *
2380 GGCTTTATCGATTTAAGGTTGAGGATTTGGTGCTTAGGGTTCGATTA
1 GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTTAGGATTCAATTA
* *
2427 GACTTTATTGATTTAAGGTT
1 GGCTTTATTGATTTAGGGTT
2447 TAAAGTTTAG
Statistics
Matches: 236, Mismatches: 58, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
46 9 0.04
47 221 0.94
48 5 0.02
49 1 0.00
ACGTcount: A:0.23, C:0.08, G:0.26, T:0.43
Consensus pattern (47 bp):
GGCTTTATTGATTTAGGGTTGAGGGTTTAGTGCTTAGGATTCAATTA
Found at i:2640 original size:14 final size:14
Alignment explanation
Indices: 2557--2676 Score: 57
Period size: 14 Copynumber: 8.6 Consensus size: 14
2547 TGGCACGGTA
*
2557 TGGCGTTTTCGATG
1 TGGCGTTATCGATG
* *
2571 TGACGTTACTTG-TG
1 TGGCGTTA-TCGATG
*
2585 TGGTGTTATC-AGTG
1 TGGCGTTATCGA-TG
* * *
2599 TGACATTATCGGTG
1 TGGCGTTATCGATG
* *
2613 TGGCGTTTTTGATG
1 TGGCGTTATCGATG
*
2627 TGGTGTTATCGATG
1 TGGCGTTATCGATG
* *
2641 TGACGTTACCTG-TG
1 TGGCGTTATC-GATG
* *
2655 TGGCATTATCGGTG
1 TGGCGTTATCGATG
*
2669 TGACGTTA
1 TGGCGTTA
2677 CCAGTCAGGT
Statistics
Matches: 74, Mismatches: 26, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
13 2 0.03
14 69 0.93
15 3 0.04
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.41
Consensus pattern (14 bp):
TGGCGTTATCGATG
Found at i:2656 original size:28 final size:28
Alignment explanation
Indices: 2625--2698 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
2615 GCGTTTTTGA
*
2625 TGTGGTGTTATCGATGTGACGTTACCTG
1 TGTGGTGTTATCGATGTGACGTTACCAG
** *
2653 TGTGGCATTATCGGTGTGACGTTACCAG
1 TGTGGTGTTATCGATGTGACGTTACCAG
** *
2681 TCAGGTGTTACCGATGTG
1 TGTGGTGTTATCGATGTG
2699 GCATTACTGG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (28 bp):
TGTGGTGTTATCGATGTGACGTTACCAG
Found at i:2724 original size:14 final size:14
Alignment explanation
Indices: 2707--2749 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
2697 TGGCATTACT
*
2707 GGTATAGCGTTATC
1 GGTATAGCATTATC
*
2721 GGTATAGCATTAAC
1 GGTATAGCATTATC
*
2735 AGTATAGCATTATC
1 GGTATAGCATTATC
2749 G
1 G
2750 ATCAGGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (14 bp):
GGTATAGCATTATC
Done.