Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006862.1 Kokia drynarioides strain JFW-HI SEQ_121461, 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: 71680
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:1476 original size:15 final size:15
Alignment explanation
Indices: 1451--1485 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1441 ACAAAAATTT
1451 AATAT-AATATTAAA
1 AATATAAATATTAAA
*
1465 AATATAAATATTTAA
1 AATATAAATATTAAA
1480 AATATA
1 AATATA
1486 TATGTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATAAATATTAAA
Found at i:1902 original size:19 final size:19
Alignment explanation
Indices: 1878--1917 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1868 TAAAAAATAT
1878 TTATAAAAT-TTAAATTTAA
1 TTATAAAATATT-AATTTAA
1897 TTATAAAATATTAATTTAA
1 TTATAAAATATTAATTTAA
1916 TT
1 TT
1918 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATAAAATATTAATTTAA
Found at i:4439 original size:31 final size:32
Alignment explanation
Indices: 4393--4452 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
4383 ATTTATATCA
*
4393 ATTTGTTGGGTAATTTTCAAGCTTTGATAATG
1 ATTTGTTGGGTAATTTTCAAGCTCTGATAATG
4425 ATTTGTT-GGTAATTTTCAAGCTCTGATA
1 ATTTGTTGGGTAATTTTCAAGCTCTGATA
4453 TTCATCCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (32 bp):
ATTTGTTGGGTAATTTTCAAGCTCTGATAATG
Found at i:5053 original size:67 final size:67
Alignment explanation
Indices: 4937--5068 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
4927 ATAAACACTG
* * * *
4937 AGCTCTGATTTGGTGTTTGAATTGAGTCTCATTCACTCTTTTAGTTAGTATGTTAGGCTGGTTGC
1 AGCTCTGATTAGGTGTTTGAACTGAGTCTCATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
5002 TA
66 TA
* *
5004 AGCTTTGATTAGGTGTTTGAACTGAGTCTCGTTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
1 AGCTCTGATTAGGTGTTTGAACTGAGTCTCATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
5069 ACGGTGTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.43
Consensus pattern (67 bp):
AGCTCTGATTAGGTGTTTGAACTGAGTCTCATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
TA
Found at i:7053 original size:30 final size:34
Alignment explanation
Indices: 7000--7060 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 34
6990 TATTATATTA
7000 TATTTGGATATATAAATGTTTATT-TATAAAATT
1 TATTTGGATATATAAATGTTTATTATATAAAATT
7033 TATTTGGA-ATAT-AA-GTTTATTATATAAA
1 TATTTGGATATATAAATGTTTATTATATAAA
7061 TAATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 7 0.26
31 8 0.30
32 4 0.15
33 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (34 bp):
TATTTGGATATATAAATGTTTATTATATAAAATT
Found at i:8261 original size:18 final size:18
Alignment explanation
Indices: 8238--8288 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
8228 ATATATCTAA
8238 ATATAATTAATATAAATT
1 ATATAATTAATATAAATT
*
8256 ATATAATT-A-GT---TT
1 ATATAATTAATATAAATT
8269 ATATAATTAATATAAATT
1 ATATAATTAATATAAATT
8287 AT
1 AT
8289 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
15 1 0.04
16 1 0.04
17 1 0.04
18 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAATTAATATAAATT
Found at i:8272 original size:22 final size:23
Alignment explanation
Indices: 8247--8294 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
8237 AATATAATTA
8247 ATATAAATT-ATAT-AATTAGTTT
1 ATAT-AATTAATATAAATTAGTTT
*
8269 ATATAATTAATATAAATTATTTT
1 ATATAATTAATATAAATTAGTTT
8292 ATA
1 ATA
8295 AAAAAACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 8 0.35
23 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATAATTAATATAAATTAGTTT
Found at i:15847 original size:113 final size:113
Alignment explanation
Indices: 15644--15873 Score: 343
Period size: 113 Copynumber: 2.0 Consensus size: 113
15634 ATCTTCTTCC
* * * *
15644 CTTTTGATTCCAATATTTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAATCTATTAAC
1 CTTTTAATTCCAATATTTTTAGTTACAAATCTATCTCAAAACTTGAATCTTTAAAACCCATTAAC
* * * * *
15709 CAAAATATTCGATATCTTTGGTTCCAATATATTCTTCCCGTTAAGTTT
66 CAAAAAATTCAATATATTTGATTCCAATATATTCTTCCCATTAAGTTT
* **
15757 CTTTTAATTCTAATATTTTTAGTTACAAATCTATCTCAAAGTTTGAATCTTTAAAACCCATTAAC
1 CTTTTAATTCCAATATTTTTAGTTACAAATCTATCTCAAAACTTGAATCTTTAAAACCCATTAAC
*
15822 CAAAAAATTCAATATATTTGATTCCAATATATTCTTCCTATTAAGTTT
66 CAAAAAATTCAATATATTTGATTCCAATATATTCTTCCCATTAAGTTT
15870 CTTT
1 CTTT
15874 GGGTTAATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 104 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (113 bp):
CTTTTAATTCCAATATTTTTAGTTACAAATCTATCTCAAAACTTGAATCTTTAAAACCCATTAAC
CAAAAAATTCAATATATTTGATTCCAATATATTCTTCCCATTAAGTTT
Found at i:18593 original size:13 final size:13
Alignment explanation
Indices: 18575--18606 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
18565 TCACTTGTTA
18575 AAAAAAATAAAAT
1 AAAAAAATAAAAT
18588 AAAAAAATAAAAT
1 AAAAAAATAAAAT
18601 AGAAAA
1 A-AAAA
18607 TTTATGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:35281 original size:27 final size:27
Alignment explanation
Indices: 35235--35287 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
35225 ACTGTAGTAA
*
35235 TATTTTAATTTGACATATTTAATTTTT
1 TATTTTAATTCGACATATTTAATTTTT
*
35262 TATTTTAATTCGA-ATAATTTTATTTT
1 TATTTTAATTCGACAT-ATTTAATTTT
35288 ATTTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (27 bp):
TATTTTAATTCGACATATTTAATTTTT
Found at i:35299 original size:16 final size:16
Alignment explanation
Indices: 35278--35309 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35268 AATTCGAATA
*
35278 ATTTTATTTTATTTAT
1 ATTTTATTTTACTTAT
35294 ATTTTATTTTACTTAT
1 ATTTTATTTTACTTAT
35310 TTCGATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTATTTTACTTAT
Found at i:47138 original size:52 final size:52
Alignment explanation
Indices: 47047--47343 Score: 425
Period size: 52 Copynumber: 5.7 Consensus size: 52
47037 ATTTCATTTC
* * * * * **
47047 ATTCGTATACTCACGATGACACATAGCCACCGTATCTCATAATCCCTAAAGG
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
**
47099 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCCCTAAAGG
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
*
47151 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAATG
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
* * * *
47203 ATTCATATACTCACGATGATATATAGCCATC-AACCTCATAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
* * *
47254 ATTCATATACTCACGATGACACATAACCATCAGTCCTTATAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
*
47306 ATTCATATACTCACGATGACACATATCCATCGGACCTC
1 ATTCATATACTCACGATGACACATAACCATCGGACCTC
47344 TTTTCATTTA
Statistics
Matches: 221, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
51 46 0.21
52 175 0.79
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
Found at i:47279 original size:103 final size:104
Alignment explanation
Indices: 47047--47343 Score: 416
Period size: 103 Copynumber: 2.9 Consensus size: 104
47037 ATTTCATTTC
* * * * * **
47047 ATTCGTATACTCACGATGACACATAGCCACCGTATCTCATAATCCCTAAAGGATTCATATACTCA
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGGATTCATATACTCA
*
47112 CGATGACACATAACCATCGGACCTCATAATCCCTAAAGG
66 CGATGACACATAACCATCGAACCTCATAATCCCTAAAGG
*
47151 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAATGATTCATATACTCA
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGGATTCATATACTCA
* * * **
47216 CGATGATATATAGCCATC-AACCTCATAATCTGTAAAGG
66 CGATGACACATAACCATCGAACCTCATAATCCCTAAAGG
* * *
47254 ATTCATATACTCACGATGACACATAACCATCAGTCCTTATAATCTGTAAAGGATTCATATACTCA
1 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGGATTCATATACTCA
* *
47319 CGATGACACATATCCATCGGACCTC
66 CGATGACACATAACCATCGAACCTC
47344 TTTTCATTTA
Statistics
Matches: 170, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
103 93 0.55
104 77 0.45
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (104 bp):
ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGGATTCATATACTCA
CGATGACACATAACCATCGAACCTCATAATCCCTAAAGG
Found at i:63963 original size:34 final size:34
Alignment explanation
Indices: 63925--63990 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
63915 GTCCTAGACC
* *
63925 TATTAGGCCCGAAAAATGAGTTTGGATAAAAATA
1 TATTAGGCCCGAAAAATAAATTTGGATAAAAATA
*
63959 TATTAGGCTCGAAAAATAAATTTGGATAAAAA
1 TATTAGGCCCGAAAAATAAATTTGGATAAAAA
63991 AATAGGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (34 bp):
TATTAGGCCCGAAAAATAAATTTGGATAAAAATA
Found at i:64091 original size:16 final size:18
Alignment explanation
Indices: 64052--64085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64042 TAAATTTATG
64052 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
64069 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
64086 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:65336 original size:44 final size:44
Alignment explanation
Indices: 65279--65363 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
65269 TTTGAGGACT
* * *
65279 TTTTTTATGCATTTTGAAAGTTCAAG-TACCTAATTGAGTGAGCC
1 TTTTTGATACATTTTGAAAGTTC-AGTTACCCAATTGAGTGAGCC
65323 TTTTTGATACATTTTGAAAGTTCAGTTACCCAATTGAGTGA
1 TTTTTGATACATTTTGAAAGTTCAGTTACCCAATTGAGTGA
65364 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (44 bp):
TTTTTGATACATTTTGAAAGTTCAGTTACCCAATTGAGTGAGCC
Found at i:65715 original size:29 final size:28
Alignment explanation
Indices: 65680--65749 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
65670 TTATTGAATA
65680 TAAATTTTGAAATATAAAAAAAAATAAAT
1 TAAATTTT-AAATATAAAAAAAAATAAAT
* * *
65709 TAAATTTTTAAATATAAAAATATATAGAT
1 TAAA-TTTTAAATATAAAAAAAAATAAAT
65738 TAAATTTTAAAT
1 TAAATTTTAAAT
65750 TTACAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.22
29 25 0.68
30 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
TAAATTTTAAATATAAAAAAAAATAAAT
Found at i:65956 original size:17 final size:17
Alignment explanation
Indices: 65934--65976 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
65924 AAAATTTTAT
*
65934 TATTTATGAAAATAATG
1 TATTTATGAAAATAATC
*
65951 TATTTATTAAAATAATC
1 TATTTATGAAAATAATC
65968 TATTT-TGAA
1 TATTTATGAA
65977 TAGTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
TATTTATGAAAATAATC
Done.