Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007353.1 Kokia drynarioides strain JFW-HI SEQ_121969, 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: 3762
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Found at i:1576 original size:12 final size:12
Alignment explanation
Indices: 1561--1586 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1551 TTTAATTTTA
1561 ATTTTAAAAAAT
1 ATTTTAAAAAAT
1573 ATTTTAAAAAAT
1 ATTTTAAAAAAT
1585 AT
1 AT
1587 AATATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTTAAAAAAT
Found at i:2537 original size:57 final size:56
Alignment explanation
Indices: 2437--2557 Score: 149
Period size: 57 Copynumber: 2.2 Consensus size: 56
2427 CGAAAATTTG
* * *
2437 AGAAAAAAAATTTAGTGTTGGTCATGCAATGACCGACACCCCCTTTTTTATCTGAT
1 AGAAAAAAAATTTAGTATTGGCCATGCAATGACCGACACCCCCTTTTTAATCTGAT
* *
2493 AGGAAAAAAAATTTTGGTATTGGCCATTGC-ATGGCCGACA-CCCCTTTTTAATCTGAT
1 A-GAAAAAAAA-TTTAGTATTGGCCA-TGCAATGACCGACACCCCCTTTTTAATCTGAT
2550 A-AAAAAAA
1 AGAAAAAAA
2558 TCAAATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
55 7 0.12
56 1 0.02
57 26 0.46
58 20 0.35
59 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (56 bp):
AGAAAAAAAATTTAGTATTGGCCATGCAATGACCGACACCCCCTTTTTAATCTGAT
Found at i:2678 original size:59 final size:59
Alignment explanation
Indices: 2570--3003 Score: 308
Period size: 59 Copynumber: 7.2 Consensus size: 59
2560 AAATTTTTGC
* * * * *
2570 ATGGCCGACATCCCCTTTTTGTCAGATAAAAAACTC-AATCTTTTGGTGTTGGCCATGCA
1 ATGGCCGACA-CCCCTTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATGCA
* * * *
2629 ATGACCGACACCCCTATCTATCTGATAAAAAAATCAAATTTTTTTGTGTTGTCCATGCA
1 ATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATGCA
* * * * * *
2688 ATGGTCGACACCTCTTTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATACA
1 ATGGCCGACACCCCTTTTTATCTGATAAAAAAA--TC-AAATTTTTTTGTGTTGGCCATGCA
* * * *
2750 ATGGCCGACACCCCCTTTTT-T-TAGATAAAAAACTTTCAAAAATTTTTGGTGTTGGTCATGTC-
1 ATGGCCGACA-CCCCTTTTTATCT-GATAAAAAA--ATC-AAATTTTTTTGTGTTGGCCATG-CA
* * ** *
2812 ATGG-CGACACCCTCTTTTTTATCTGATAAAAAAAT-TAATTTATTTGCATTGACCATGCA
1 ATGGCCGACACCC-C-TTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATGCA
* * * * * * *
2871 ATGGTCGACACTCCATTTT-TGTGAAATAAAAAATTCAAATTTTTTTTGTGTTGGTCATGCC
1 ATGGCCGACACCCCTTTTTATCTG--ATAAAAAAATCAAA-TTTTTTTGTGTTGGCCATGCA
** * * * * * *
2932 ATGATCGACATCCCCTTTTTATTTGGT-AAAATATTAAATTTTTTTTGTGTAGGCCATGTA
1 ATGGCCGACA-CCCCTTTTTATCTGATAAAAAAATCAAA-TTTTTTTGTGTTGGCCATGCA
2992 ATGGCCGACACC
1 ATGGCCGACACC
3004 AACTTTCCCT
Statistics
Matches: 294, Mismatches: 60, Indels: 42
0.74 0.15 0.11
Matches are distributed among these distances:
57 3 0.01
58 25 0.09
59 85 0.29
60 46 0.16
61 34 0.12
62 78 0.27
63 22 0.07
64 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (59 bp):
ATGGCCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATGCA
Found at i:2852 original size:121 final size:119
Alignment explanation
Indices: 2567--3003 Score: 356
Period size: 121 Copynumber: 3.6 Consensus size: 119
2557 ATCAAATTTT
* * * *
2567 TGCATGGCCGACATCCCCTTTTTGTCAGAT-AAAAAACTCAATCTTTTGGTGTTGGCCATGCAAT
1 TGCATGGCCGACATCCCCTTTTTATCAGATAAAAAAATTAAATTTTTTGGTGTTGGCCATGCAAT
* * * *
2631 GACCGACA-CCCCTATCTATCT-GATAAAAAAATC-AAATTTTTTTGTGTT-GTCCA
66 GGCCGACACCCCCT-T-TTTTTAGATAAAAAATTCAAAATTTTTTTGTGTTGGT-CA
* * * *
2684 TGCAATGGTCGACA-CCTCTTTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATA
1 TGC-ATGGCCGACATCCCCTTTTTATCAGATAAAAAAA-TT--AAATTTTTTGGTGTTGGCCATG
* *
2748 CAATGGCCGACACCCCCTTTTTTTAGATAAAAAACTTTCAAAAATTTTTGGTGTTGGTCA
62 CAATGGCCGACACCCCCTTTTTTTAGATAAAAAA--TTCAAAATTTTTTTGTGTTGGTCA
* ** *
2808 TGTCATGG-CGACA-CCCTCTTTTTTATCTGATAAAAAAATT-AATTTATTT-GCATTGACCATG
1 TG-CATGGCCGACATCCC-C-TTTTTATCAGATAAAAAAATTAAATTT-TTTGGTGTTGGCCATG
* * * * * *
2869 CAATGGTCGACACTCCATTTTTGTGAAATAAAAAATTCAAATTTTTTTTGTGTTGGTCA
62 CAATGGCCGACACCCCCTTTTT-TTAGATAAAAAATTCAAAATTTTTTTGTGTTGGTCA
** ** * * * * *
2928 TGCCATGATCGACATCCCCTTTTTATTTGGT-AAAATATTAAATTTTTTTTGTGTAGGCCATGTA
1 TG-CATGGCCGACATCCCCTTTTTATCAGATAAAAAAATTAAA-TTTTTTGGTGTTGGCCATGCA
2992 ATGGCCGACACC
64 ATGGCCGACACC
3004 AACTTTCCCT
Statistics
Matches: 259, Mismatches: 40, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
117 17 0.07
118 15 0.06
119 8 0.03
120 45 0.17
121 100 0.39
122 21 0.08
123 9 0.03
124 24 0.09
125 20 0.08
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (119 bp):
TGCATGGCCGACATCCCCTTTTTATCAGATAAAAAAATTAAATTTTTTGGTGTTGGCCATGCAAT
GGCCGACACCCCCTTTTTTTAGATAAAAAATTCAAAATTTTTTTGTGTTGGTCA
Done.