Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010699.1 Kokia drynarioides strain JFW-HI SEQ_125646, 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: 3239
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:468 original size:12 final size:12
Alignment explanation
Indices: 442--498 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
432 GGGACCAACG
* *
442 AAAAATGAAGGA
1 AAAAAAGAAAGA
454 AAAAAA-AAAGA
1 AAAAAAGAAAGA
465 AAAAAGAGAAAGA
1 AAAAA-AGAAAGA
*
478 AAGAAAGAAAGA
1 AAAAAAGAAAGA
*
490 AAGAAAGAA
1 AAAAAAGAA
499 GAAGGAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.22
12 22 0.55
13 9 0.22
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:478 original size:4 final size:4
Alignment explanation
Indices: 460--498 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
450 AGGAAAAAAA
*
460 AAAG AAAA AAGAG AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG AA
499 GAAGGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:922 original size:20 final size:21
Alignment explanation
Indices: 881--925 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
871 TAATTTACTT
881 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
902 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
922 TAAT
1 TAAT
926 AGTAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:1218 original size:30 final size:30
Alignment explanation
Indices: 1184--1290 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
1174 TAAACTTAGC
1184 TAATTAATTACCAAAATATAATATAAAAAA
1 TAATTAATTACCAAAATATAATATAAAAAA
* ****
1214 TAATTAATTATC-AAA-ATAATAT-CCCCA
1 TAATTAATTACCAAAATATAATATAAAAAA
1241 TCATATT-ATTGACCAAAATATAATATAAAAAA
1 T-A-ATTAATT-ACCAAAATATAATATAAAAAA
*
1273 TAATTAATTATCAAAATA
1 TAATTAATTACCAAAATA
1291 ATATCCCATC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.03
28 11 0.19
29 8 0.14
30 25 0.42
31 11 0.19
32 2 0.03
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (30 bp):
TAATTAATTACCAAAATATAATATAAAAAA
Found at i:1229 original size:16 final size:16
Alignment explanation
Indices: 1184--1233 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1174 TAAACTTAGC
*
1184 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
1200 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
1214 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
1230 TAAT
1 TAAT
1234 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:1307 original size:58 final size:59
Alignment explanation
Indices: 1193--1315 Score: 230
Period size: 59 Copynumber: 2.1 Consensus size: 59
1183 CTAATTAATT
1193 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
*
1252 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATAT-CCCATCATATTATTT
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
1310 ACCAAA
1 ACCAAA
1316 GTAAATAATG
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 20 0.32
59 43 0.68
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.32
Consensus pattern (59 bp):
ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
Done.