Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002959.1 Kokia drynarioides strain JFW-HI SEQ_115430, 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: 34456
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:7256 original size:21 final size:21
Alignment explanation
Indices: 7232--7283 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
7222 TGAGACAATA
*
7232 CTACTGATACAAGT-GTGACTT
1 CTACTGATACAAGTCATG-CTT
* * *
7253 CTACCGAAACATGTCATGCTT
1 CTACTGATACAAGTCATGCTT
7274 CTACTGATAC
1 CTACTGATAC
7284 TAAAAACTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (21 bp):
CTACTGATACAAGTCATGCTT
Found at i:11055 original size:156 final size:153
Alignment explanation
Indices: 10841--11476 Score: 710
Period size: 156 Copynumber: 4.1 Consensus size: 153
10831 AAAAAATTAA
* * *
10841 AATTGAAT-ATTCTGTTTC-GAGATTTATTTCTACCATTCAACAGAATTTATTCGATTTTTTTTC
1 AATTAAATAATTCTGTTTCAG-GATTTATTCCTACCATTCAACAGAATTTATTCTATTTTTTTTC
* * * * *
10904 AAAATAAGAATTAATTAAATAATTCTGTTTTAGGA-TTATTTCTGTCGTTCAATAGAATTTATTC
65 AAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAATAGAATTGA---
** * **
10968 TATTTTTTTTTGTTTTCAAATGAGAATT
127 T-TTTGATTTTGTTTCCAAACAAGAATT
*
10996 AATTAAATAATTCTGTTTCAGGATTTATTCCTATCATTCAACAGAATTTATTCTATTTTTTTGTT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTACCATTCAACAGAATTTATTCTA--TTTTT-TT
* * * *
11061 TCCAAACAAAAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTACCGCTCAATAGAATTGAT
63 TCAAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAATAGAATTGAT
11126 TTTGATTTTGTTTCCAAACAAGAATT
128 TTTGATTTTGTTTCCAAACAAGAATT
* * * *
11152 AATTAAATAATTCTATTTCAGGATTTATTTCTGCCATTCAATAGAATTTATTCTATTTTTTGTAT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTACCATTCAACAGAATTTATTCTATTTTTT-T-T
* * *
11217 CCAAAA-AAGAATTAATTAAATAATTCTGTTTCAGGATTTACTCCTGCCGTTCAA-AAAAATGAT
64 -CAAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAATAGAATTGAT
11280 TTTGATTTTGTTTCCAAACAAGAATT
128 TTTGATTTTGTTTCCAAACAAGAATT
* * ** ** * * *
11306 AATCAAATAATTCTGTTTCAAGATTTATTCCTGTCGCTCTACA-AATTTGATTTTAATTTTGTTT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTACCATTCAACAGAATTT-ATTCT-ATTTTTTTT
* * * * * * * *
11370 CCAAACAAGAATTATTTAAATAATTCTATTTCAGAAATTATTCATGTCGTTCAACAGAATTGATT
64 CAAAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAATAGAATTGATT
*
11435 TTGATTTTGTTTCCAAATAAGAATT
129 TTGATTTTGTTTCCAAACAAGAATT
*
11460 -ATTAAATAATTTTGTTT
1 AATTAAATAATTCTGTTT
11477 TAGAATTTTA
Statistics
Matches: 414, Mismatches: 54, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
152 4 0.01
153 63 0.15
154 110 0.27
155 58 0.14
156 116 0.28
157 2 0.00
158 5 0.01
159 35 0.08
160 21 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (153 bp):
AATTAAATAATTCTGTTTCAGGATTTATTCCTACCATTCAACAGAATTTATTCTATTTTTTTTCA
AAACAAGAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAATAGAATTGATTTT
GATTTTGTTTCCAAACAAGAATT
Found at i:11175 original size:77 final size:77
Alignment explanation
Indices: 10841--11476 Score: 640
Period size: 77 Copynumber: 8.2 Consensus size: 77
10831 AAAAAATTAA
* * * * * * *
10841 AATTGAAT-ATTCTGTTTC-GAGATTTATTTCTACCATTCAACAGAATTTA-TTCGATTTTTTTT
1 AATTAAATAATTCTGTTTCAG-GATTTATTCCTGCCGTTCAACAGAATTGATTTTGATTTTGTTT
* *
10903 CAAAATAAGAATT
65 CCAAACAAGAATT
* * * * * **
10916 AATTAAATAATTCTGTTTTAGGA-TTATTTCTGTCGTTCAATAGAATTTATTCTATTTTTTTTTG
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGA---T-TTTGATTTTG
* **
10980 TTTTCAAATGAGAATT
62 TTTCCAAACAAGAATT
** * * **
10996 AATTAAATAATTCTGTTTCAGGATTTATTCCTATCATTCAACAGAATTTATTCTATTTTTTTGTT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGATT-T-TGATTTTGTT
*
11061 TCCAAACAAAAATT
64 TCCAAACAAGAATT
* * *
11075 AATTAAATAATTCTGTTTCAGGATTTATTCCTACCGCTCAATAGAATTGATTTTGATTTTGTTTC
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGATTTTGATTTTGTTTC
11140 CAAACAAGAATT
66 CAAACAAGAATT
* * * * * * *
11152 AATTAAATAATTCTATTTCAGGATTTATTTCTGCCATTCAATAGAATTTATTCTAT-TTTTTGTA
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGATT-T-TGATTTTGTT
*
11216 TCCAAAAAAGAATT
64 TCCAAACAAGAATT
* * *
11230 AATTAAATAATTCTGTTTCAGGATTTACTCCTGCCGTTCAA-AAAAATGATTTTGATTTTGTTTC
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGATTTTGATTTTGTTTC
11294 CAAACAAGAATT
66 CAAACAAGAATT
* * * * * *
11306 AATCAAATAATTCTGTTTCAAGATTTATTCCTGTCGCTCTACA-AATTTGATTTTAATTTTGTTT
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAA-TTGATTTTGATTTTGTTT
11370 CCAAACAAGAATT
65 CCAAACAAGAATT
* * * * * *
11383 ATTTAAATAATTCTATTTCAGAAATTATTCATGTCGTTCAACAGAATTGATTTTGATTTTGTTTC
1 AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGATTTTGATTTTGTTTC
*
11448 CAAATAAGAATT
66 CAAACAAGAATT
*
11460 -ATTAAATAATTTTGTTT
1 AATTAAATAATTCTGTTT
11477 TAGAATTTTA
Statistics
Matches: 474, Mismatches: 71, Indels: 31
0.82 0.12 0.05
Matches are distributed among these distances:
75 30 0.06
76 82 0.17
77 169 0.36
78 62 0.13
79 68 0.14
80 41 0.09
81 22 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (77 bp):
AATTAAATAATTCTGTTTCAGGATTTATTCCTGCCGTTCAACAGAATTGATTTTGATTTTGTTTC
CAAACAAGAATT
Found at i:11333 original size:231 final size:233
Alignment explanation
Indices: 10849--11476 Score: 761
Period size: 231 Copynumber: 2.7 Consensus size: 233
10839 AAAATTGAAT
* * ** * * * * *
10849 ATTCTGTTTCGAGATTTATTTCTACCATTCAACAGAATTTA-TTCGATTTTTTTTCAAAATAAGA
1 ATTCTGTTTCAAGATTTATTCCTACCGCTCAACAGAATTGATTTTGATTTTGTTTCCAAACAAGA
* *
10913 ATTAATTAAATAATTCTGTTTTAGGATTATTTCTGTCGTTCAATAGAATTTATTCTATTTTTTTT
66 ATTAATTAAATAATTCTATTTCAGGATTATTTCTGTCGTTCAATAGAATTTATTCTA---TTTTT
* * * * * *
10978 TGTTTTCAAATGAGAATTAATTAAATAATTCTGTTTCAGGATTTATTCCTATCATTCAACAGAAT
128 TGTTTCCAAATAAGAATTAATTAAATAATTCTGTTTCAGGATTTACTCCTACCATTCAACAAAAA
* ** *
11043 TTATTCTATTTTTTTGTTTCCAAACAAAAATTAATTAAATA
193 TGATTCTATGATTTTGTTTCCAAACAAAAATTAATCAAATA
* *
11084 ATTCTGTTTCAGGATTTATTCCTACCGCTCAATAGAATTGATTTTGATTTTGTTTCCAAACAAGA
1 ATTCTGTTTCAAGATTTATTCCTACCGCTCAACAGAATTGATTTTGATTTTGTTTCCAAACAAGA
* *
11149 ATTAATTAAATAATTCTATTTCAGGATTTATTTCTGCCATTCAATAGAATTTATTCTATTTTTTG
66 ATTAATTAAATAATTCTATTTCAGGA-TTATTTCTGTCGTTCAATAGAATTTATTCTATTTTTTG
* * * *
11214 TATCCAAAAAAGAATTAATTAAATAATTCTGTTTCAGGATTTACTCCTGCCGTTCAA-AAAAATG
130 TTTCCAAATAAGAATTAATTAAATAATTCTGTTTCAGGATTTACTCCTACCATTCAACAAAAATG
*
11278 ATT-T-TGATTTTGTTTCCAAACAAGAATTAATCAAATA
195 ATTCTATGATTTTGTTTCCAAACAAAAATTAATCAAATA
** * *
11315 ATTCTGTTTCAAGATTTATTCCTGTCGCTCTACA-AATTTGATTTTAATTTTGTTTCCAAACAAG
1 ATTCTGTTTCAAGATTTATTCCTACCGCTCAACAGAA-TTGATTTTGATTTTGTTTCCAAACAAG
* * * * *
11379 AATTATTTAAATAATTCTATTTCAGAAATTA-TTCATGTCGTTCAACAGAATTGATT-T-TGATT
65 AATTAATTAAATAATTCTATTTCAG-GATTATTTC-TGTCGTTCAATAGAATTTATTCTAT-TTT
*
11441 TTGTTTCCAAATAAGAATT-ATTAAATAATTTTGTTT
127 TTGTTTCCAAATAAGAATTAATTAAATAATTCTGTTT
11477 TAGAATTTTA
Statistics
Matches: 341, Mismatches: 46, Indels: 18
0.84 0.11 0.04
Matches are distributed among these distances:
229 17 0.05
230 25 0.07
231 128 0.38
232 2 0.01
233 7 0.02
234 56 0.16
235 34 0.10
236 43 0.13
237 29 0.09
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (233 bp):
ATTCTGTTTCAAGATTTATTCCTACCGCTCAACAGAATTGATTTTGATTTTGTTTCCAAACAAGA
ATTAATTAAATAATTCTATTTCAGGATTATTTCTGTCGTTCAATAGAATTTATTCTATTTTTTGT
TTCCAAATAAGAATTAATTAAATAATTCTGTTTCAGGATTTACTCCTACCATTCAACAAAAATGA
TTCTATGATTTTGTTTCCAAACAAAAATTAATCAAATA
Found at i:18672 original size:16 final size:16
Alignment explanation
Indices: 18626--18671 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
18616 TTAGTCACTT
**
18626 GAAAAAGGAA-AATGA
1 GAAAAAGGAAGAAAAA
18641 GAAAAAGGAAGAAAAA
1 GAAAAAGGAAGAAAAA
18657 GAAAAA-GAAGAAAAA
1 GAAAAAGGAAGAAAAA
18672 ATTTATGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (16 bp):
GAAAAAGGAAGAAAAA
Found at i:29810 original size:34 final size:34
Alignment explanation
Indices: 29772--29891 Score: 141
Period size: 34 Copynumber: 3.5 Consensus size: 34
29762 TGTTACAGTG
* * *
29772 ATTTGGTGTGTTGGATGGAATAGGTCTTATGAGC
1 ATTTGGTGTGTTGGATGGACTAGCTCTTACGAGC
* * *
29806 ATTTGGTGTGTTGGATAGACCAGCTCCTACGAGC
1 ATTTGGTGTGTTGGATGGACTAGCTCTTACGAGC
* * * *
29840 ATTTGGTGTGTTCGATCGACTAGCTCTTACAAGT
1 ATTTGGTGTGTTGGATGGACTAGCTCTTACGAGC
*
29874 ATTTGGTGTGTTGAATGG
1 ATTTGGTGTGTTGGATGG
29892 TTAACTGTGT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 71 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (34 bp):
ATTTGGTGTGTTGGATGGACTAGCTCTTACGAGC
Done.