Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008647.1 Kokia drynarioides strain JFW-HI SEQ_123328, 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: 12303
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:331 original size:28 final size:29
Alignment explanation
Indices: 298--364 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
288 ATAATTCTTT
* *
298 TTATAAAAATAATATTAAAAAT-AATTAA
1 TTATAAAAATAAGATGAAAAATAAATTAA
* *
326 TTATAAAAATAAGGTGAAGAATAAATTAA
1 TTATAAAAATAAGATGAAAAATAAATTAA
355 TTATAGAAAA
1 TTATA-AAAA
365 GGGCATTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 18 0.55
29 11 0.33
30 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (29 bp):
TTATAAAAATAAGATGAAAAATAAATTAA
Found at i:1206 original size:21 final size:21
Alignment explanation
Indices: 1180--1221 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1170 TATATAAATA
*
1180 TTTTTTTC-CTATTTTAGTTTT
1 TTTTTTTCTCT-TTTTAATTTT
1201 TTTTTTTCTCTTTTTAATTTT
1 TTTTTTTCTCTTTTTAATTTT
1222 GCTTTGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTCTCTTTTTAATTTT
Found at i:1609 original size:42 final size:42
Alignment explanation
Indices: 1555--1642 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
1545 TAATTCCAAA
*
1555 ATGGATAAAAAAATTAACCTTTTTTTAACTTTCCTAATGTGGC
1 ATGGATGAAAAAATTAA-CTTTTTTTAACTTTCCTAATGTGGC
*
1598 ATGGATGAAAAAATTAACTTTTTTTAACTTTCTTAATGTGGC
1 ATGGATGAAAAAATTAACTTTTTTTAACTTTCCTAATGTGGC
1640 ATG
1 ATG
1643 CACGTGGGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 27 0.63
43 16 0.37
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (42 bp):
ATGGATGAAAAAATTAACTTTTTTTAACTTTCCTAATGTGGC
Found at i:5817 original size:6 final size:6
Alignment explanation
Indices: 5808--5837 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5798 GATGAAGAGG
*
5808 AAGGGA AAGGGA AAGGAA AAGGGA AAGGGA
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA
5838 GAGCAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:9767 original size:28 final size:29
Alignment explanation
Indices: 9735--9795 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
9725 ATAATCCTTT
* *
9735 TTATAAAAATAATATTAAAAAT-AATTAA
1 TTATAAAAATAAGATGAAAAATAAATTAA
*
9763 TTATAAAAATAAGGTGAAAAATAAATTAA
1 TTATAAAAATAAGATGAAAAATAAATTAA
9792 TTAT
1 TTAT
9796 GGAAAAAGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (29 bp):
TTATAAAAATAAGATGAAAAATAAATTAA
Found at i:10124 original size:20 final size:21
Alignment explanation
Indices: 10071--10126 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
10061 AAAATAATTT
*
10071 TATTTAATATAAATGTATTAAAA
1 TATTTAATATAAA--TATAAAAA
*
10094 TAATTAGATATAAA-ATAAAAA
1 TATTTA-ATATAAATATAAAAA
10115 TATTTAATATAA
1 TATTTAATATAA
10127 TTTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
23 5 0.17
24 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
TATTTAATATAAATATAAAAA
Found at i:10650 original size:21 final size:21
Alignment explanation
Indices: 10624--10665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10614 TATATAAATA
*
10624 TTTTTTTC-CTATTTTAGTTTT
1 TTTTTTTCTCT-TTTTAATTTT
10645 TTTTTTTCTCTTTTTAATTTT
1 TTTTTTTCTCTTTTTAATTTT
10666 GCTTTGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTCTCTTTTTAATTTT
Found at i:11088 original size:42 final size:43
Alignment explanation
Indices: 11028--11109 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
11018 AATGGATAAA
11028 AAAAAATTAACGTTTTTTTAACTTT-TCTAATGTGGCATGGATG
1 AAAAAATTAACGTTTTTTTAACTTTCT-TAATGTGGCATGGATG
*
11071 AAAAAATTAACTTTTTTTTAACTTTCTTAATGTGGCATG
1 AAAAAATTAACGTTTTTTTAACTTTCTTAATGTGGCATG
11110 CACGTGGGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (43 bp):
AAAAAATTAACGTTTTTTTAACTTTCTTAATGTGGCATGGATG
Done.