Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009477.1 Kokia drynarioides strain JFW-HI SEQ_124185, 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: 38104
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1238 original size:30 final size:29
Alignment explanation
Indices: 1199--1525 Score: 268
Period size: 30 Copynumber: 11.0 Consensus size: 29
1189 GATGAATTTA
1199 GGGTTAAAATGTAATTTTGGAAAAGTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTG
* * *
1228 GTGGTAAAAATGTAAATTTT-GAAAATTTTAT
1 G-GGTTAAAATGT-AATTTTGGAAAAGTTT-G
*
1259 GGGTTAAAATGTAATTTTAGG-AAATTTTG
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTG
* ** *
1288 AGGTTAAAATGTGGTTTTAGGAATA-TTTG
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTG
** * *
1317 GCATTGAAAATGCAATTTAAGG-AAAGTTTAG
1 GGGTT-AAAATGTAATTT-TGGAAAAGTTT-G
* *
1348 GGGTTAAAA-GATGATTTTGGGAAAGTTTAG
1 GGGTTAAAATG-TAATTTTGGAAAAGTTT-G
* *
1378 GGGTTAAAAAGAAATTTTGGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-G
* *
1408 GGGTTAAAATGTAAATTTGGAAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTG
* * *
1437 AGGTTAAAATGTAGTTTTAGAAAAGTTTGG
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-G
*
1467 AGGGTTAAAATGTAATTTTGGAAAAGATTG
1 -GGGTTAAAATGTAATTTTGGAAAAGTTTG
** *
1497 AGGGTTAAAATCAAATTTTGAAAAAGTTT
1 -GGGTTAAAATGTAATTTTGGAAAAGTTT
1526 AAGGACCTTT
Statistics
Matches: 241, Mismatches: 42, Indels: 29
0.77 0.13 0.09
Matches are distributed among these distances:
29 60 0.25
30 144 0.60
31 37 0.15
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTG
Found at i:1472 original size:90 final size:90
Alignment explanation
Indices: 1198--1526 Score: 302
Period size: 90 Copynumber: 3.7 Consensus size: 90
1188 CGATGAATTT
* * *
1198 AGGGTTAAAATGTAATTTTGGAAAAGTTTGGTGGTAAAAATGTAAATTTTGAAAATTTTATG-GG
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTGG-GGTTAAAATGTAAATTTGGAAAAGTTTA-GAGG
* *
1262 TTAAAATGTAATTTTAGGAAA-TTTTG
64 TTAAAATGTAGTTTTAGGAAAGTTTAG
** * ** * *
1288 A-GGTTAAAATGTGGTTTTAGGAATA-TTTGGCATTGAAAATG-CAATTTAAGG-AAAGTTTAGG
1 AGGGTTAAAATGTAATTTT-GGAAAAGTTTGGGGTT-AAAATGTAAATTT--GGAAAAGTTTAGA
*
1349 GGTTAAAA-G-ATGATTTTGGGAAAGTTTAG
62 GGTTAAAATGTA-G-TTTTAGGAAAGTTTAG
* *
1378 -GGGTTAAAAAGAAATTTTGGAAAAGTTTAGGGGTTAAAATGTAAATTTGGAAAAGTTTA-AGGT
1 AGGGTTAAAATGTAATTTTGGAAAAGTTT-GGGGTTAAAATGTAAATTTGGAAAAGTTTAGAGGT
* *
1441 TAAAATGTAGTTTTAGAAAAGTTTGG
65 TAAAATGTAGTTTTAGGAAAGTTTAG
* * *
1467 AGGGTTAAAATGTAATTTTGGAAAAGATTGAGGGTTAAAAT-CAAATTTTGAAAAAGTTTA
1 AGGGTTAAAATGTAATTTTGGAAAAGTTTG-GGGTTAAAATGTAAA-TTTGGAAAAGTTTA
1527 AGGACCTTTT
Statistics
Matches: 192, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
87 1 0.01
88 8 0.04
89 82 0.43
90 91 0.47
91 10 0.05
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.36
Consensus pattern (90 bp):
AGGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTAAATTTGGAAAAGTTTAGAGGTT
AAAATGTAGTTTTAGGAAAGTTTAG
Found at i:2171 original size:20 final size:19
Alignment explanation
Indices: 2143--2183 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2133 AAAAAATTCA
*
2143 AATGGATATGTATATATATG
1 AATGGATATATATATA-ATG
*
2163 AATGTATATATATATAATG
1 AATGGATATATATATAATG
2182 AA
1 AA
2184 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (19 bp):
AATGGATATATATATAATG
Found at i:3872 original size:51 final size:52
Alignment explanation
Indices: 3767--3873 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 52
3757 AGAAATTGTG
* *
3767 AAATGGAGAAATAAGAAACATTTGGAAATGATTAAGGGTTTTTCCAAAATGA
1 AAATGGAGAAATAAGAAACATTTGGAAATGAATAAGGGTTTCTCCAAAATGA
* * **
3819 AAATGGAGAAATGA-AAATATTTGGAAATGAATGTGGGTTTCTCCAAAATGA
1 AAATGGAGAAATAAGAAACATTTGGAAATGAATAAGGGTTTCTCCAAAATGA
3870 AAAT
1 AAAT
3874 TAAAAATGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 36 0.73
52 13 0.27
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (52 bp):
AAATGGAGAAATAAGAAACATTTGGAAATGAATAAGGGTTTCTCCAAAATGA
Found at i:3886 original size:51 final size:51
Alignment explanation
Indices: 3767--3887 Score: 136
Period size: 51 Copynumber: 2.4 Consensus size: 51
3757 AGAAATTGTG
* * * * *
3767 AAATGGAGAAATAAGAAACATTTGGAAATGATTAAGGGTTTTTCCAAAATGA
1 AAATGGAAAAATGA-AAATATTTGGAAATGAATAAGGGTTTCTCCAAAATGA
* **
3819 AAATGGAGAAATGAAAATATTTGGAAATGAATGTGGGTTTCTCCAAAATGA
1 AAATGGAAAAATGAAAATATTTGGAAATGAATAAGGGTTTCTCCAAAATGA
*
3870 AAAT-TAAAAATGGAAAAT
1 AAATGGAAAAAT-GAAAAT
3888 GAAAATTATC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 5 0.08
51 42 0.70
52 13 0.22
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (51 bp):
AAATGGAAAAATGAAAATATTTGGAAATGAATAAGGGTTTCTCCAAAATGA
Found at i:7946 original size:13 final size:13
Alignment explanation
Indices: 7924--7954 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
7914 TCAACACTAA
7924 TTCT-CATTTTCT
1 TTCTCCATTTTCT
7936 TTCTCCATTTTCT
1 TTCTCCATTTTCT
7949 TTCTCC
1 TTCTCC
7955 TCCAAGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (13 bp):
TTCTCCATTTTCT
Found at i:14158 original size:18 final size:18
Alignment explanation
Indices: 14132--14167 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
14122 AGTAAATTAC
*
14132 AATTTAAAATAGAGTATT
1 AATTAAAAATAGAGTATT
*
14150 AATTAAAAATAGTGTATT
1 AATTAAAAATAGAGTATT
14168 GATGAGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (18 bp):
AATTAAAAATAGAGTATT
Found at i:26182 original size:28 final size:28
Alignment explanation
Indices: 26150--26219 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 28
26140 AAACATGATA
*
26150 GAAAAGAATAATCTTTATGGTAAATTTT
1 GAAAAGAATAATCTTTATGGAAAATTTT
* *
26178 GAAAAGAAT-A-GTTTGTGGAAAATTTT
1 GAAAAGAATAATCTTTATGGAAAATTTT
* *
26204 GAAAATAATAGTCTTT
1 GAAAAGAATAATCTTT
26220 GTAGCAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 21 0.62
27 1 0.03
28 12 0.35
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (28 bp):
GAAAAGAATAATCTTTATGGAAAATTTT
Found at i:26236 original size:28 final size:28
Alignment explanation
Indices: 26205--26277 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
26195 GAAAATTTTG
* *
26205 AAAATAATAGTCTTTGTAGCAAACTCTA
1 AAAAGAATAGTCCTTGTAGCAAACTCTA
* *
26233 AAAAGAATGGTCCTTGTGGCAAACTCTA
1 AAAAGAATAGTCCTTGTAGCAAACTCTA
* * *
26261 GAACGAATAGCCCTTGT
1 AAAAGAATAGTCCTTGT
26278 GGCGTACTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (28 bp):
AAAAGAATAGTCCTTGTAGCAAACTCTA
Found at i:30370 original size:20 final size:20
Alignment explanation
Indices: 30306--30371 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
30296 AAAAAAAATA
**
30306 AAAAATTATGAGGAAATACC
1 AAAAATTATGAGGGGATACC
** * * *
30326 AAAAGAAACATGAAGGGAAATC
1 -AAA-AATTATGAGGGGATACC
30348 AAAAATTATGAGGGGATACC
1 AAAAATTATGAGGGGATACC
30368 AAAA
1 AAAA
30372 GTTGGTCTTA
Statistics
Matches: 32, Mismatches: 12, Indels: 3
0.68 0.26 0.06
Matches are distributed among these distances:
20 16 0.50
21 6 0.19
22 10 0.31
ACGTcount: A:0.56, C:0.09, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAAATTATGAGGGGATACC
Done.