Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005570.1 Kokia drynarioides strain JFW-HI SEQ_119683, 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: 13399
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:606 original size:20 final size:21
Alignment explanation
Indices: 564--610 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 21
554 CTCAACAAAT
564 TAAAAATATTTATACTTTTTTAAA
1 TAAAAATATTTATAC---TTTAAA
588 TAAAAATATTTATAC-TTAAA
1 TAAAAATATTTATACTTTAAA
608 TAA
1 TAA
611 CACTAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
24 15 0.65
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAATATTTATACTTTAAA
Found at i:1115 original size:33 final size:31
Alignment explanation
Indices: 1076--1144 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
1066 AGTTCAAAGT
*
1076 AAAAAATTATTAAAATTAT-ATGTCAATAATATA
1 AAAAAATTATTAAAA-TATCAT-TAAATAAT-TA
1109 AAAAAATTATTAAAATATCATTAAATAATTA
1 AAAAAATTATTAAAATATCATTAAATAATTA
1140 AAAAA
1 AAAAA
1145 TACCATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.21
32 10 0.29
33 17 0.50
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (31 bp):
AAAAAATTATTAAAATATCATTAAATAATTA
Found at i:2039 original size:29 final size:31
Alignment explanation
Indices: 1977--2042 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
1967 TTTGATATTA
* *
1977 AAACTTGACATTTTTTCTTAATTTGGTACCT
1 AAACTTGACATCTTTTCTTAAGTTGGTACCT
*
2008 AAACTTGACA-CTTTT-TTAAGTTGGTACTT
1 AAACTTGACATCTTTTCTTAAGTTGGTACCT
2037 AAACTT
1 AAACTT
2043 TTTGGAATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 18 0.56
30 4 0.12
31 10 0.31
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (31 bp):
AAACTTGACATCTTTTCTTAAGTTGGTACCT
Found at i:2058 original size:88 final size:89
Alignment explanation
Indices: 1907--2097 Score: 230
Period size: 88 Copynumber: 2.1 Consensus size: 89
1897 TTAATATAAT
** * * *
1907 ATTTGGTATTTAAATTTTACACTATTTTCTAATTTGGTACCTAAACTTTTTTTGGTCCAATTTGA
1 ATTTGGTACCTAAACTTGACACTATTTTCTAAGTTGGTACCTAAAC-TTTTTTGGTCCAATTTGA
1972 TA-TTAAAACTTGACAT-TTTTTCTTA
65 TACTT-AAACTTGAC-TCTTTTTCTTA
*
1997 ATTTGGTACCTAAACTTGACACT-TTTT-TAAGTTGGTACTTAAAC-TTTTTGGAATCCAATTTG
1 ATTTGGTACCTAAACTTGACACTATTTTCTAAGTTGGTACCTAAACTTTTTTGG--TCCAATTTG
*
2059 ATACTTGAACTTGACTCTTTTTCTTA
64 ATACTTAAACTTGACTCTTTTTCTTA
*
2085 ATTTGATACCTAA
1 ATTTGGTACCTAA
2098 TTTTTTAATA
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
86 7 0.08
87 1 0.01
88 56 0.63
89 6 0.07
90 19 0.21
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (89 bp):
ATTTGGTACCTAAACTTGACACTATTTTCTAAGTTGGTACCTAAACTTTTTTGGTCCAATTTGAT
ACTTAAACTTGACTCTTTTTCTTA
Found at i:2312 original size:60 final size:58
Alignment explanation
Indices: 2238--2431 Score: 185
Period size: 60 Copynumber: 3.3 Consensus size: 58
2228 AATATTTAAT
* * * *
2238 AAGTTTAGGTACCAAATTGAACTAAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTC
1 AAGTTCAGGTACCAAATTG-GCT-AAAAAAAGTTTAAGTACCAAATTAGAAAAAAATGTC
* * * * *
2298 AAGTTCAGGTACCAAATTGGGTCCAAAAAACGTTTATGTACTAAATTA-AGAAAAAGTGTC
1 AAGTTCAGGTACCAAATT-GG-CTAAAAAAAGTTTAAGTACCAAATTAGA-AAAAAATGTC
* * * *
2358 AAGTTCAAGTACCAAATTGGCT-AAAAAATTTTAAGTATCAAATTAGAAAAAAAAATGTT
1 AAGTTCAGGTACCAAATTGGCTAAAAAAAGTTTAAGTACCAAATTAG--AAAAAAATGTC
*
2417 AAGTTCATGTACCAA
1 AAGTTCAGGTACCAA
2432 TTTAAGTTCA
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
57 18 0.16
58 1 0.01
59 25 0.23
60 64 0.58
61 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (58 bp):
AAGTTCAGGTACCAAATTGGCTAAAAAAAGTTTAAGTACCAAATTAGAAAAAAATGTC
Found at i:2429 original size:59 final size:61
Alignment explanation
Indices: 2279--2471 Score: 168
Period size: 60 Copynumber: 3.2 Consensus size: 61
2269 GCTTAGGTAC
* *
2279 CAAATTAG--AAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCCAAAAAACGTTTATGTA
1 CAAATTAGAAAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTCCAAAAAACGTTTAAGTA
* * * *
2338 CTAAATT--AAGAAAAAGTGTCAAGTTCAAGTACCAAATT-GG-CTAAAAAA-TTTTAAGTA
1 C-AAATTAGAAAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTCCAAAAAACGTTTAAGTA
* * * ** * * *
2395 TCAAATTAGAAAAAAAAATGTTAAGTTCATGTACCAATTTAAGTTCAATAAACATTT-AGATA
1 -CAAATTAGAAAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTCCAAAAAACGTTTAAG-TA
2457 TCAAATTAGAAAAAA
1 -CAAATTAGAAAAAA
2472 GTATCAATTT
Statistics
Matches: 108, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
57 12 0.11
58 8 0.07
59 29 0.27
60 32 0.30
61 7 0.06
62 20 0.19
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (61 bp):
CAAATTAGAAAAAAAAATGTCAAGTTCAAGTACCAAATTGGGTCCAAAAAACGTTTAAGTA
Found at i:2463 original size:119 final size:117
Alignment explanation
Indices: 2279--2493 Score: 256
Period size: 119 Copynumber: 1.8 Consensus size: 117
2269 GCTTAGGTAC
** *
2279 CAAATTAGAAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCCAAAAAACGTTTATGTACTAAAT
1 CAAATTAGAAAAAAATGTCAAGTTCAGGTACCAAATTAAGTCCAAAAAACATTTATGTACTAAAT
* *
2344 TA-AGAAAAAGTGTCAAGTTCAAGTACCAAATTGGCTAAAAAATTTTAAGTAT
66 TAGA-AAAAAGTATCAAGTTAAAGTACCAAATTGGCTAAAAAATTTTAAGTAT
* * * * *
2396 CAAATTAGAAAAAAAAATGTTAAGTTCATGTACCAATTTAAGTTCAATAAACATTTA-GATA-TC
1 CAAATTAG--AAAAAAATGTCAAGTTCAGGTACCAAATTAAGTCCAAAAAACATTTATG-TACT-
* *
2459 AAATTAGAAAAAAGTATCAATTTAAAGTATCAAAT
62 AAATTAGAAAAAAGTATCAAGTTAAAGTACCAAAT
2494 GTTATATTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
117 8 0.10
118 2 0.02
119 70 0.86
120 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.29
Consensus pattern (117 bp):
CAAATTAGAAAAAAATGTCAAGTTCAGGTACCAAATTAAGTCCAAAAAACATTTATGTACTAAAT
TAGAAAAAAGTATCAAGTTAAAGTACCAAATTGGCTAAAAAATTTTAAGTAT
Done.