Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014390.1 Kokia drynarioides strain JFW-HI SEQ_129428, 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: 15277
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Found at i:10008 original size:20 final size:18
Alignment explanation
Indices: 9985--10028 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
9975 GTCCTAATTA
9985 TAAAAATTTTAATAAAATC
1 TAAAAATTTTAA-AAAATC
* *
10004 TTAAATATTTTAAAAATTC
1 -TAAAAATTTTAAAAAATC
10023 TAAAAA
1 TAAAAA
10029 GTAAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAATTTTAAAAAATC
Found at i:10255 original size:18 final size:18
Alignment explanation
Indices: 10232--10270 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
10222 AAGACACAAG
10232 AACAGTACTATACCTTGA
1 AACAGTACTATACCTTGA
*
10250 AACAGTACTATAGCTTGA
1 AACAGTACTATACCTTGA
10268 AAC
1 AAC
10271 TGGTATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (18 bp):
AACAGTACTATACCTTGA
Found at i:11530 original size:28 final size:27
Alignment explanation
Indices: 11499--11559 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
11489 AAAATGAGAC
* *
11499 TTTTGGACATCGGGGGGCAAAATGGTAA
1 TTTTGGA-ATCGCGAGGCAAAATGGTAA
* * *
11527 TTTTGGATTCTCGAGGTAAAATGGTAA
1 TTTTGGAATCGCGAGGCAAAATGGTAA
11554 TTTTGG
1 TTTTGG
11560 GAAATTTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.26, C:0.08, G:0.31, T:0.34
Consensus pattern (27 bp):
TTTTGGAATCGCGAGGCAAAATGGTAA
Found at i:11690 original size:29 final size:28
Alignment explanation
Indices: 11652--11969 Score: 280
Period size: 29 Copynumber: 10.9 Consensus size: 28
11642 GATCTTAGAG
*
11652 GTTCGAGGGTAAAAATGAAATTTTTGGAA
1 GTTCG-GGGTAAAAATGGAATTTTTGGAA
* **
11681 GTTTCGGGGTCAAAACAGAATTTTTGGAA
1 G-TTCGGGGTAAAAATGGAATTTTTGGAA
*
11710 GTTTC-GGGTCAAAAAATGGGATTTTTGGAA
1 G-TTCGGGGT--AAAAATGGAATTTTTGGAA
** *
11740 GTTCGGGGGTATGAATGAAATTTTTGGAA
1 GTTC-GGGGTAAAAATGGAATTTTTGGAA
*
11769 GTTTTGGGGTCAAAAATGGAATTTTTGGAA
1 G-TTCGGGGT-AAAAATGGAATTTTTGGAA
** *
11799 GTTCAAGGTCAAAATGGAATTTTTGGAA
1 GTTCGGGGTAAAAATGGAATTTTTGGAA
*
11827 GTTCGAGGGT-AAAATGGAATTTTTAGAAA
1 GTTCG-GGGTAAAAATGGAATTTTT-GGAA
* * *
11856 TTTTGGGGGTGAAAATGGAATTTTTGGAA
1 -GTTCGGGGTAAAAATGGAATTTTTGGAA
* * *
11885 GTTCGAGGGTGAAAATGGAAGTTTTGGAT
1 GTTCG-GGGTAAAAATGGAATTTTTGGAA
* *
11914 GTTTTGGGATCAAAAATGGAATTTTTGGAA
1 G-TTCGGGGT-AAAAATGGAATTTTTGGAA
* *
11944 GCTCGGGGGTAAAAATGTAATTTTTG
1 GTTC-GGGGTAAAAATGGAATTTTTG
11970 AATAGTTTAG
Statistics
Matches: 235, Mismatches: 39, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
28 43 0.18
29 108 0.46
30 80 0.34
31 4 0.02
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (28 bp):
GTTCGGGGTAAAAATGGAATTTTTGGAA
Found at i:11871 original size:58 final size:59
Alignment explanation
Indices: 11652--11968 Score: 231
Period size: 59 Copynumber: 5.4 Consensus size: 59
11642 GATCTTAGAG
* * * * *
11652 GTTCGAGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGTCAAAACA--GAATTTTTGGAA
1 GTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGGGATCAAAA-ATGGAATTTTTGGAA
* * * ** * ** *
11710 GTTTC--GGGTCAAAAAATGGGATTTTTGGAAGTTCGGGGGT-ATGAATGAAATTTTTGGAA
1 G-TTCGAGGGT--AAAAATGGAATTTTTAGAAATTTTGGGATCAAAAATGGAATTTTTGGAA
* * * ***
11769 GTTTTG-GGGTCAAAAATGGAATTTTTGGAAGTTCAAGG-TC-AAAATGGAATTTTTGGAA
1 G-TTCGAGGGT-AAAAATGGAATTTTTAGAAATTTTGGGATCAAAAATGGAATTTTTGGAA
* *
11827 GTTCGAGGGT-AAAATGGAATTTTTAGAAATTTTGGGGGT-GAAAATGGAATTTTTGGAA
1 GTTCGAGGGTAAAAATGGAATTTTTAGAAATTTT-GGGATCAAAAATGGAATTTTTGGAA
* * * **
11885 GTTCGAGGGTGAAAATGGAAGTTTTGGATGTTTTGGGATCAAAAATGGAATTTTTGGAA
1 GTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGGGATCAAAAATGGAATTTTTGGAA
* * *
11944 GCTCGGGGGTAAAAATGTAATTTTT
1 GTTCGAGGGTAAAAATGGAATTTTT
11969 GAATAGTTTA
Statistics
Matches: 214, Mismatches: 32, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
56 19 0.09
57 10 0.05
58 57 0.27
59 124 0.58
60 4 0.02
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
GTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTGGGATCAAAAATGGAATTTTTGGAA
Found at i:11910 original size:145 final size:146
Alignment explanation
Indices: 11663--11944 Score: 372
Period size: 145 Copynumber: 1.9 Consensus size: 146
11653 TTCGAGGGTA
* * *
11663 AAAATGAAATTTTTGGAAGTTTCGGGGTCAAAACAGAATTTTTGGAAGTTTCGGGTCAAAAAATG
1 AAAATGAAATTTTTGGAAGTTTCGGGGTCAAAACAGAATTTTTAGAAATTTCGGGGCAAAAAATG
* * * * *
11728 GGATTTTTGGAAGTTCGGGGGTATGAATGAAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTT
66 GAATTTTTGGAAGTTCGAGGGTATAAATGAAAGTTTTGGAAGTTTTGGGATCAAAAATGGAATTT
11793 TTGGAAGTTCAAGGTC
131 TTGGAAGTTCAAGGTC
* ** * ***
11809 AAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAATGGAATTTTTAGAAATTTTGGGGGTGAAAAT
1 AAAATGAAATTTTTGGAAGTTTCG-GGGTCAAAACAGAATTTTTAGAAATTTCGGGGCAAAAAAT
* *
11872 GGAATTTTTGGAAGTTCGAGGGTGA-AAATGGAAGTTTTGGATGTTTTGGGATCAAAAATGGAAT
65 GGAATTTTTGGAAGTTCGAGGGT-ATAAATGAAAGTTTTGGAAGTTTTGGGATCAAAAATGGAAT
11936 TTTTGGAAG
129 TTTTGGAAG
11945 CTCGGGGGTA
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
145 94 0.80
146 23 0.20
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (146 bp):
AAAATGAAATTTTTGGAAGTTTCGGGGTCAAAACAGAATTTTTAGAAATTTCGGGGCAAAAAATG
GAATTTTTGGAAGTTCGAGGGTATAAATGAAAGTTTTGGAAGTTTTGGGATCAAAAATGGAATTT
TTGGAAGTTCAAGGTC
Found at i:13073 original size:31 final size:31
Alignment explanation
Indices: 13040--13101 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
13030 TCTTTTTTTA
*
13040 TTAA-TAATTAATAATATTATTATTATTATTA
1 TTAATTAA-TAATAATAATATTATTATTATTA
13071 TTAATTAATAATAATAATATTATTATTATTA
1 TTAATTAATAATAATAATATTATTATTATTA
13102 AAATAGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTAATTAATAATAATAATATTATTATTATTA
Found at i:13075 original size:28 final size:28
Alignment explanation
Indices: 13037--13102 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
13027 GTTTCTTTTT
* * *
13037 TTATTAATAATTAATAATATTATTATTA
1 TTATTATTAATTAATAATAATAATATTA
13065 TTATTATTAATTAATAATAATAATATTA
1 TTATTATTAATTAATAATAATAATATTA
13093 TTATTATTAA
1 TTATTATTAA
13103 AATAGTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATTATTAATTAATAATAATAATATTA
Found at i:13116 original size:3 final size:3
Alignment explanation
Indices: 13054--13101 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
13044 TAATTAATAA
* * * *
13054 TAT TAT TAT TAT TAT TAT TAAT TAA TAA TAA TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
13100 TA
1 TA
13102 AAATAGTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TAT
Done.