Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012653.1 Kokia drynarioides strain JFW-HI SEQ_127664, 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: 32496
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2380 original size:18 final size:18
Alignment explanation
Indices: 2353--2390 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2343 TAAATTTTCA
*
2353 AATTCGAAT-AACTTGAAT
1 AATTCAAATAAAC-TGAAT
2371 AATTCAAATAAACTGAAT
1 AATTCAAATAAACTGAAT
2389 AA
1 AA
2391 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.29
Consensus pattern (18 bp):
AATTCAAATAAACTGAAT
Found at i:3080 original size:99 final size:99
Alignment explanation
Indices: 2868--3152 Score: 267
Period size: 99 Copynumber: 2.9 Consensus size: 99
2858 TCACCCTTAG
* * **
2868 TTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTGCAGGATTCGTCGTTGTGGCCTCAATCCT
1 TTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTGCAGGATTCGCCATTGCAGCCTCAATCCT
*
2933 TCCCATCATATCTTCTAAGGTATCGAGCTCACCG
66 TCCCATCATATCTTCTAAGGTATCGAGCTCACCA
** * * * * *
2967 TTATGGCCTTAACCTTTCCCTTCATATCTTCATGGTATC-GGGTTTGCCATTGCAGCCTCAATCC
1 TTGCGACCTCAACCTTTCCCTTCATATCTTCATGGT-GCAGGATTCGCCATTGCAGCCTCAATCC
* * * *
3031 TTCCCATCACGTAT-TT-TAAGGTATTGGGTTCGCCA
65 TTCCCATCA--TATCTTCTAAGGTATCGAGCTCACCA
* * * * * * *
3066 TTGCGACCTCAACCTTTCCCTTCAT-TC-TCATAGTACTA-GATCCGCCGTTGCGGCCTCGATCT
1 TTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTGC-AGGATTCGCCATTGCAGCCTCAATCC
* *
3128 TTCCCGTCATGTCTTCTAAGGTATC
65 TTCCCATCATATCTTCTAAGGTATC
3153 AGGTTTGTCG
Statistics
Matches: 147, Mismatches: 32, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
95 2 0.01
96 3 0.02
97 39 0.27
98 2 0.01
99 95 0.65
100 3 0.02
101 3 0.02
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.35
Consensus pattern (99 bp):
TTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTGCAGGATTCGCCATTGCAGCCTCAATCCT
TCCCATCATATCTTCTAAGGTATCGAGCTCACCA
Found at i:16187 original size:17 final size:17
Alignment explanation
Indices: 16160--16194 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
16150 GGTTCAATGA
16160 TTTCTTTTTC-TATTTT
1 TTTCTTTTTCTTATTTT
16176 TTTCTATTTTCTTATTTT
1 TTTCT-TTTTCTTATTTT
16194 T
1 T
16195 AAAACGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 5 0.29
18 7 0.41
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTTCTTATTTT
Found at i:24922 original size:57 final size:57
Alignment explanation
Indices: 24861--24979 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 57
24851 AACAATCTAG
* * * **
24861 GACATCAAAACAACAACCAT-TATTCACATTTTGATAACATAAATATGTGCATTAAGA
1 GACATCAAAACAACAACCATAAATT-ACATTTGGACAACATAAATATGCACATTAAGA
* ** * *
24918 GACATTATGACAACAACTATAAATTACATTTGGACAGCATAAATATGCACATTAAGA
1 GACATCAAAACAACAACCATAAATTACATTTGGACAACATAAATATGCACATTAAGA
24975 GACAT
1 GACAT
24980 TTTGACAGCA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
57 48 0.94
58 3 0.06
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (57 bp):
GACATCAAAACAACAACCATAAATTACATTTGGACAACATAAATATGCACATTAAGA
Found at i:24980 original size:57 final size:57
Alignment explanation
Indices: 24898--25018 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 57
24888 ATTTTGATAA
** **
24898 CATAAATATGTGCATTAAGAGACATTATGACAACAACTATAAATTACATTTGGACAG
1 CATAAATATGCACATTAAGAGACATTATGACAACAACTATAAATTACATTAAGACAG
* *
24955 CATAAATATGCACATTAAGAGACATTTTGACAGCAACTATAAATTACATTAAGACAG
1 CATAAATATGCACATTAAGAGACATTATGACAACAACTATAAATTACATTAAGACAG
25012 CATAAAT
1 CATAAAT
25019 GTATAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (57 bp):
CATAAATATGCACATTAAGAGACATTATGACAACAACTATAAATTACATTAAGACAG
Found at i:27634 original size:17 final size:17
Alignment explanation
Indices: 27574--27635 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
27564 TTACAAGAAT
*
27574 ATGAAAGGTTGAGGAAG
1 ATGAAAGGTTAAGGAAG
27591 ATGAAAGGTTAAAGGTCAAG
1 ATGAAAGGTT-AAGG--AAG
**
27611 --GGGAGGTTAAGGAAG
1 ATGAAAGGTTAAGGAAG
27626 ATGAAAGGTT
1 ATGAAAGGTT
27636 GAACATCCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
15 3 0.09
17 20 0.57
18 9 0.26
20 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.39, T:0.19
Consensus pattern (17 bp):
ATGAAAGGTTAAGGAAG
Found at i:31928 original size:12 final size:11
Alignment explanation
Indices: 31904--31943 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
31894 GTTTTGTTTA
31904 ATTTAATTTTT
1 ATTTAATTTTT
*
31915 ATTTGATTTGTT
1 ATTTAATTT-TT
31927 ATTTAATTTTTT
1 ATTTAA-TTTTT
31939 ATTTA
1 ATTTA
31944 GTTGAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.32
12 14 0.56
13 3 0.12
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:32234 original size:17 final size:17
Alignment explanation
Indices: 32212--32244 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32202 TTATTTTGTA
32212 TCATTTTGGTAAATAAC
1 TCATTTTGGTAAATAAC
*
32229 TCATTTTGGTATATAA
1 TCATTTTGGTAAATAA
32245 TTATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (17 bp):
TCATTTTGGTAAATAAC
Found at i:32462 original size:3 final size:3
Alignment explanation
Indices: 32454--32496 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
32444 AAAATTAAAC
32454 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.