Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013373.1 Kokia drynarioides strain JFW-HI SEQ_128396, 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: 114185
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:3723 original size:26 final size:25
Alignment explanation
Indices: 3682--3743 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
3672 ATCATGAAAA
*
3682 AATTTTAAATAGAC-TTAAAATATATTT
1 AATTTTAAATAAACTTTAAAA-A-A-TT
3709 AA-TTTAAATAAACTTTAAAAAATT
1 AATTTTAAATAAACTTTAAAAAATT
3733 AATTTTAAATA
1 AATTTTAAATA
3744 GATTTGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.12
25 9 0.28
26 11 0.34
27 8 0.25
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (25 bp):
AATTTTAAATAAACTTTAAAAAATT
Found at i:10226 original size:12 final size:13
Alignment explanation
Indices: 10203--10236 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
10193 GAATCCAATC
10203 AAAATCGAAAATG
1 AAAATCGAAAATG
10216 AAAAT-GAAAATG
1 AAAATCGAAAATG
10228 AAAATCGAA
1 AAAATCGAA
10237 TAAATCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATCGAAAATG
Found at i:10255 original size:7 final size:7
Alignment explanation
Indices: 10199--10256 Score: 52
Period size: 6 Copynumber: 8.6 Consensus size: 7
10189 ATCAGAATCC
10199 AATC-AA
1 AATCGAA
10205 AATCGAA
1 AATCGAA
10212 AAT-GAA
1 AATCGAA
10218 AAT-GAA
1 AATCGAA
10224 AAT-GAA
1 AATCGAA
10230 AATCGAATA
1 AATCG-A-A
**
10239 AATCCTA
1 AATCGAA
10246 AATCGAA
1 AATCGAA
10253 AATC
1 AATC
10257 ACAATCAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
6 22 0.50
7 16 0.36
8 1 0.02
9 5 0.11
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.19
Consensus pattern (7 bp):
AATCGAA
Found at i:15938 original size:6 final size:6
Alignment explanation
Indices: 15929--15955 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15919 TGGATTTGGA
15929 AAATGG AAATGG AAATGG AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAA
15956 ACCTTGTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:21621 original size:17 final size:17
Alignment explanation
Indices: 21599--21636 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
21589 TGTTTCTGAA
*
21599 TAATTTAACT-AATTTAT
1 TAATTTAAATCAATTT-T
21616 TAATTTAAATCAATTTT
1 TAATTTAAATCAATTTT
21633 TAAT
1 TAAT
21637 AAATAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTAAATCAATTTT
Found at i:30174 original size:22 final size:22
Alignment explanation
Indices: 30149--30200 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
30139 GTAACTTTAA
30149 TTGAATTTATTTTAATTTCAAT
1 TTGAATTTATTTTAATTTCAAT
30171 TTGAATTTATTTTAATTTCAAT
1 TTGAATTTATTTTAATTTCAAT
30193 TTGAATTT
1 TTGAATTT
30201 GAAAAGAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.60
Consensus pattern (22 bp):
TTGAATTTATTTTAATTTCAAT
Found at i:41191 original size:11 final size:11
Alignment explanation
Indices: 41175--41204 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
41165 CAAGGTGGCC
41175 AAAAGAAAGAA
1 AAAAGAAAGAA
41186 AAAAGAAAGAA
1 AAAAGAAAGAA
41197 AAAAGAAA
1 AAAAGAAA
41205 AGATAGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:50577 original size:3 final size:3
Alignment explanation
Indices: 50569--50605 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
50559 TTGAGGAGTG
50569 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
50606 TAAGAAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56844 original size:12 final size:11
Alignment explanation
Indices: 56811--56888 Score: 56
Period size: 12 Copynumber: 7.1 Consensus size: 11
56801 GTTATTAAAT
56811 ATAATTTAATA
1 ATAATTTAATA
* *
56822 AAAATGATAATGA
1 ATAAT-TTAAT-A
*
56835 ATAATTTAATC
1 ATAATTTAATA
56846 AT-ATTT--TA
1 ATAATTTAATA
56854 ATAA-TTAATA
1 ATAATTTAATA
*
56864 AAAATGTTAATA
1 ATAAT-TTAATA
56876 TATAATTTAATA
1 -ATAATTTAATA
56888 A
1 A
56889 CATTTTTAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
8 5 0.10
9 1 0.02
10 9 0.18
11 7 0.14
12 20 0.39
13 9 0.18
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (11 bp):
ATAATTTAATA
Found at i:56863 original size:42 final size:43
Alignment explanation
Indices: 56811--56899 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 43
56801 GTTATTAAAT
56811 ATAATTTAATAAAAATGATAATGA-ATAATTTAAT-CATATTTTA
1 ATAATTTAATAAAAATGATAAT-ATATAATTTAATACAT-TTTTA
*
56854 ATAA-TTAATAAAAATGTTAATATATAATTTAATAACATTTTTA
1 ATAATTTAATAAAAATGATAATATATAATTTAAT-ACATTTTTA
56897 ATA
1 ATA
56900 TAATTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
41 1 0.02
42 26 0.62
43 12 0.29
44 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (43 bp):
ATAATTTAATAAAAATGATAATATATAATTTAATACATTTTTA
Found at i:59364 original size:15 final size:16
Alignment explanation
Indices: 59346--59375 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59336 TCCTTAAAAA
59346 ATTAAAA-TAATTAAG
1 ATTAAAATTAATTAAG
59361 ATTAAAATTAATTAA
1 ATTAAAATTAATTAA
59376 AATAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTAAAATTAATTAAG
Found at i:59383 original size:16 final size:16
Alignment explanation
Indices: 59343--59384 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
59333 TTATCCTTAA
59343 AAAATTAAAA-TAATT
1 AAAATTAAAATTAATT
*
59358 AAGATTAAAATTAATT
1 AAAATTAAAATTAATT
*
59374 AAAATAAAAAT
1 AAAATTAAAAT
59385 GGTTAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAATTAAAATTAATT
Found at i:60225 original size:23 final size:23
Alignment explanation
Indices: 60185--60230 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
60175 ATTATAAAAA
*
60185 TTAATATTTTTATTAAAAATAAT
1 TTAATATTTTTATAAAAAATAAT
*
60208 TTAACTATTTTTA-AAAAATTAAT
1 TTAA-TATTTTTATAAAAAATAAT
60231 AATCAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATATTTTTATAAAAAATAAT
Found at i:60280 original size:19 final size:17
Alignment explanation
Indices: 60245--60292 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
60235 AAAATTTACC
*
60245 AAAAAATGATTAAATTAA
1 AAAAAAT-ATAAAATTAA
60263 TAAAAAATATAAACATTAA
1 -AAAAAATATAAA-ATTAA
60282 AAATAAATATA
1 AAA-AAATATA
60293 TTTCGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAAATATAAAATTAA
Found at i:67726 original size:6 final size:6
Alignment explanation
Indices: 67711--67764 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
67701 GTCCATGACA
*
67711 CCCATG CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC
1 CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC
67759 CCCATC
1 CCCATC
67765 GCTGGGGCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.17, C:0.65, G:0.02, T:0.17
Consensus pattern (6 bp):
CCCATC
Found at i:103036 original size:20 final size:19
Alignment explanation
Indices: 103011--103079 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
103001 ATAATTAAAT
103011 TTTAAATAATTAAAACATAA
1 TTTAAATAATTAAAA-ATAA
* * *
103031 TTTAAAAAATTATAATTAAA
1 TTTAAATAATTAAAAAT-AA
* * *
103051 TTAAAATATTTAAAAAACAA
1 TTTAAATAATT-AAAAATAA
103071 TTTAAATAA
1 TTTAAATAA
103080 AATATTACAA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.89
21 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTAAATAATTAAAAATAA
Found at i:104378 original size:19 final size:20
Alignment explanation
Indices: 104336--104380 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
104326 TTATTATCTT
* *
104336 ATAATTAAAACTAAAAATTA
1 ATAAATAAAACTAAAAATGA
*
104356 ATAAATAAAA-TAAAAATGC
1 ATAAATAAAACTAAAAATGA
104375 ATAAAT
1 ATAAAT
104381 CAATAATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAATAAAACTAAAAATGA
Found at i:112179 original size:4 final size:4
Alignment explanation
Indices: 112172--112236 Score: 60
Period size: 4 Copynumber: 16.0 Consensus size: 4
112162 AAATAAATAG
* * * *
112172 GAAA GAAA GAAA GGAAA AAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
112222 G-AA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA
112237 TGTAATGTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 39 0.78
5 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:112201 original size:25 final size:26
Alignment explanation
Indices: 112172--112233 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
112162 AAATAAATAG
112172 GAAAGAAAGAAAGGA-AAAAAAGAAA
1 GAAAGAAAGAAAGGAGAAAAAAGAAA
* **
112197 GAAAGGAAG-AAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGGAGAAAAAAGAAA
*
112222 G-AAGAAGGAAAG
1 GAAAGAAAGAAAG
112234 AAATGTAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (26 bp):
GAAAGAAAGAAAGGAGAAAAAAGAAA
Found at i:112215 original size:29 final size:27
Alignment explanation
Indices: 112174--112236 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
112164 ATAAATAGGA
112174 AAGAAAGAAAGGAAAAAAAGAAAGAAAGG
1 AAGAAAGAAAGGAAAAAAAG-AAG-AAGG
* * *
112203 AAGAAGGAGAGGAAAGAAAGAAGAAGG
1 AAGAAAGAAAGGAAAAAAAGAAGAAGG
112230 AAAGAAA
1 -AAGAAA
112237 TGTAATGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 17 0.59
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAGGAAAAAAAGAAGAAGG
Found at i:112217 original size:17 final size:15
Alignment explanation
Indices: 112170--112236 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
112160 GCAAATAAAT
112170 AGGAAAGAAAG-A-A
1 AGGAAAGAAAGAAGA
112183 AGG-AA-AAA-AAGA
1 AGGAAAGAAAGAAGA
* *
112195 AAGAAAGGAAGAAGGA
1 AGGAAAGAAAGAA-GA
112211 GAGGAAAGAAAGAAGA
1 -AGGAAAGAAAGAAGA
112227 AGGAAAGAAA
1 AGGAAAGAAA
112237 TGTAATGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
11 4 0.09
12 5 0.12
13 5 0.12
14 2 0.05
15 12 0.28
16 4 0.09
17 11 0.26
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGGAAAGAAAGAAGA
Done.