Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014495.1 Kokia drynarioides strain JFW-HI SEQ_129534, 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: 12217
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.36
Warning! 410 characters in sequence are not A, C, G, or T
Found at i:5201 original size:20 final size:20
Alignment explanation
Indices: 5176--5213 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5166 TTTCTAAAAA
5176 TATGTTGATGTTATTTTTAT
1 TATGTTGATGTTATTTTTAT
5196 TATGTTGATGTTATTTTT
1 TATGTTGATGTTATTTTT
5214 GTGAACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (20 bp):
TATGTTGATGTTATTTTTAT
Found at i:5532 original size:336 final size:340
Alignment explanation
Indices: 4742--6075 Score: 1717
Period size: 337 Copynumber: 4.0 Consensus size: 340
4732 AATATCGTTC
* * *
4742 AAAAAATTTAATCTGGTATTACAAAAGAA-TCCAAAATTAATTGTTGAGAAAATTGCTTTCTTTC
1 AAAAAATTTAATCTGATATTACAAAAAAATTCCAAAATTAATTGTTGAGAAAATTGCTCTCTTTC
* *
4806 CATTCCTCAATTTTTTTACAATGTTTTGATTTTCTAAAAATATGTTTATGTTATTTTTATTATGT
66 CATTCCTCAATTTTTCT-CAATGTTTTGATTTTCTAAAAATATGTTGATGTTATTTTTATTATGT
* * *
4871 TGATGTTACTTTTGTGAACTCAAATTATTAAAAATTTATATA-ATTTTGTACATATTATTAATTC
130 TGATGTTACTTTCGTGAACTCAAAATATTATAAATTTATA-AGATTTTGTACATATTATTAATTC
* * * *
4935 ATTTTATATAA-TTTT-TTTATTTTTAAATATATTATTGTCATTATTTATTTTATTTTGTTTCAC
194 ATTTTATGTAACTTTTGATT-TTTTT-AATATATTTTTGTCATTATTTATTTTATTTT-TGTCAC
4998 GTGATATA--TTT-TTA--TT--A---TTTATCATGTTTCAATTAACTCTATCATAGTAATTTAG
256 GTGATATATTTTTATTATTTTGAATTCTTTATCATGTTTCAATTAACTCTATCATAGTAATTTAG
* *
5053 TTTTAATTTTAATATCATTT
321 TTTTAACTTTAATTTCATTT
* * * * * *
5073 AAAAAATTTAATCTAATATTTC-AAAAGATTTCAAAATTAATTGTTGAGAAAATTGCTCTATTTT
1 AAAAAATTTAATCTGATATTACAAAAAAATTCCAAAATTAATTGTTGAGAAAATTGCTCTCTTTC
* *
5137 CATTCCTCAATTTTTCACAATGTTTCGATTTTCTAAAAATATGTTGATGTTATTTTTATTATGTT
66 CATTCCTCAATTTTTCTCAATGTTTTGATTTTCTAAAAATATGTTGATGTTATTTTTATTATGTT
* * *
5202 GATGTTATTTTTGTGAACTCAAAATATTATAAATTTATAAGATTTTGTACATATTATTAATTCGT
131 GATGTTACTTTCGTGAACTCAAAATATTATAAATTTATAAGATTTTGTACATATTATTAATTCAT
* * * * *
5267 TTTATGTAACTTCTG-TTTTTTTAATATATTTTTTTCATTAATTATTTTATTTTTCTCACCTGAT
196 TTTATGTAACTTTTGATTTTTTTAATATATTTTTGTCATTATTTATTTTATTTTTGTCACGTGAT
* * * * **
5331 ATA-TTTTATTATTTTTAATT-TTTATCATTTTTTAATTAACTCCATTGTAGTAATTTAGTTTTA
261 ATATTTTTATTATTTTGAATTCTTTATCATGTTTCAATTAACTCTATCATAGTAATTTAGTTTTA
5394 ACTTTAATTTCATTT
326 ACTTTAATTTCATTT
* * * * * *
5409 AAAAAATTTAATTTGATTTTTCAAAAAAATTCTAAAATTAATTGCTGAGAAAATTGTTCTCTTTC
1 AAAAAATTTAATCTGATATTACAAAAAAATTCCAAAATTAATTGTTGAGAAAATTGCTCTCTTTC
* * *
5474 CATTCCTCAATTTCTCTCAATGTTTTGATTTTCTAGAAATATGTTGATGCTA-TTTTATTATGTT
66 CATTCCTCAATTTTTCTCAATGTTTTGATTTTCTAAAAATATGTTGATGTTATTTTTATTATGTT
* * * * * *
5538 GATGTTACTTTCGTAAATTCAAAATACTATAAATTTATATGATTTTGTACCTATAATTAATTCAT
131 GATGTTACTTTCGTGAACTCAAAATATTATAAATTTATAAGATTTTGTACATATTATTAATTCAT
* * * *
5603 TTTATGTAACTTTTGACTTCTTTAATATATTTTTGTCATTATTTAATTTATTTTTGTCATGTGAT
196 TTTATGTAACTTTTGATTTTTTTAATATATTTTTGTCATTATTTATTTTATTTTTGTCACGTGAT
* * * *
5668 ATATTTTTATTATTTAGAATTCTTTATCATATTTCAGTTAACTCTATCATAGTAATTCAGTTTTA
261 ATATTTTTATTATTTTGAATTCTTTATCATGTTTCAATTAACTCTATCATAGTAATTTAGTTTTA
* **
5733 AATTT-ATTATGGTTT
326 ACTTTAATT-TCATTT
* * *
5748 AAAAAATTTAA-CTTGATTTTACAAAAAAATTCCAAAATTATTTGTCGAGAAAATTGCTCTCTTT
1 AAAAAATTTAATC-TGATATTACAAAAAAATTCCAAAATTAATTGTTGAGAAAATTGCTCTCTTT
* * * *
5812 CCATTCCTCAATTTTTCTCAAT-TTTTTATTTTCTAGAAATATGTTGGTGTTATTTTTATTATAT
65 CCATTCCTCAATTTTTCTCAATGTTTTGATTTTCTAAAAATATGTTGATGTTATTTTTATTATGT
* ** * **
5876 TGATGTGACTTTCGTGAACTCAAAATATTATAAATTTAT-ATTTTTTTTACATATTATTAATTTG
130 TGATGTTACTTTCGTGAACTCAAAATATTATAAATTTATAAGATTTTGTACATATTATTAATTCA
* * * *
5940 TTTTATGTAATTTTTGATTTTTTTAATAT-TTTTTGTTATTATTTATTTTATATTTGTCATGTGA
195 TTTTATGTAACTTTTGATTTTTTTAATATATTTTTGTCATTATTTATTTTATTTTTGTCACGTGA
*
6004 TATATTTTTATTATTTTGAATTGTTTATCATGTTTCAATTAACTCTATCATAGTAATTTAGTTTT
260 TATATTTTTATTATTTTGAATTCTTTATCATGTTTCAATTAACTCTATCATAGTAATTTAGTTTT
6069 AACTTTA
325 AACTTTA
6076 GGCATAATGA
Statistics
Matches: 871, Mismatches: 112, Indels: 33
0.86 0.11 0.03
Matches are distributed among these distances:
328 12 0.01
329 32 0.04
330 125 0.14
331 70 0.08
332 2 0.00
334 1 0.00
336 152 0.17
337 223 0.26
338 88 0.10
339 166 0.19
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (340 bp):
AAAAAATTTAATCTGATATTACAAAAAAATTCCAAAATTAATTGTTGAGAAAATTGCTCTCTTTC
CATTCCTCAATTTTTCTCAATGTTTTGATTTTCTAAAAATATGTTGATGTTATTTTTATTATGTT
GATGTTACTTTCGTGAACTCAAAATATTATAAATTTATAAGATTTTGTACATATTATTAATTCAT
TTTATGTAACTTTTGATTTTTTTAATATATTTTTGTCATTATTTATTTTATTTTTGTCACGTGAT
ATATTTTTATTATTTTGAATTCTTTATCATGTTTCAATTAACTCTATCATAGTAATTTAGTTTTA
ACTTTAATTTCATTT
Found at i:5636 original size:20 final size:21
Alignment explanation
Indices: 5613--5658 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5603 TTTATGTAAC
*
5613 TTTTGAC-TTCTTTAATATAT
1 TTTTGACATTATTTAATATAT
* *
5633 TTTTGTCATTATTTAATTTAT
1 TTTTGACATTATTTAATATAT
5654 TTTTG
1 TTTTG
5659 TCATGTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTGACATTATTTAATATAT
Found at i:5648 original size:21 final size:21
Alignment explanation
Indices: 5623--5662 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5613 TTTTGACTTC
5623 TTTAATATATTTTTGTCATTA
1 TTTAATATATTTTTGTCATTA
*
5644 TTTAATTTATTTTTGTCAT
1 TTTAATATATTTTTGTCAT
5663 GTGATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTAATATATTTTTGTCATTA
Found at i:6357 original size:30 final size:30
Alignment explanation
Indices: 6321--6400 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
6311 TAAATAATTT
*
6321 TAAAATTATTAAAATTATTTTTTTAAAAT-A
1 TAAAATTATTAAAATTA-ATTTTTAAAATAA
* *
6351 TAAAATTATTAAACTTAATTTTTGAAATAA
1 TAAAATTATTAAAATTAATTTTTAAAATAA
6381 TAAAATTATT-AAA-TAATTTT
1 TAAAATTATTAAAATTAATTTT
6401 AATTTCCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.16
29 11 0.24
30 27 0.60
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
TAAAATTATTAAAATTAATTTTTAAAATAA
Found at i:7496 original size:31 final size:29
Alignment explanation
Indices: 7461--7533 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 29
7451 ATTAAAATTA
7461 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-AAAAAAATAAT
* *
7492 TTTAATAATTGTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAAATAAT
7521 TTTAATAATTTTA
1 TTTAATAATTTTA
7534 AAATCATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 22 0.56
30 5 0.13
31 12 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATATTTAAAAAAATAAT
Found at i:7520 original size:20 final size:22
Alignment explanation
Indices: 7495--7536 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7485 AAATAATTTT
7495 AATAATTGT-AT-ATTTTAAAA
1 AATAATTGTAATAATTTTAAAA
*
7515 AATAATTTTAATAATTTTAAAA
1 AATAATTGTAATAATTTTAAAA
7537 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATAATTGTAATAATTTTAAAA
Found at i:10485 original size:3 final size:3
Alignment explanation
Indices: 10479--10520 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
10469 GTAGTAGTAG
10479 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10521 CAATCCATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10703 original size:17 final size:15
Alignment explanation
Indices: 10678--10716 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
10668 AATTTGTACA
10678 TCAATATCAACCAAGT
1 TCAATATCAACCAA-T
*
10694 TCACATATCAATCAAT
1 TCA-ATATCAACCAAT
10710 TCAATAT
1 TCAATAT
10717 GGTATTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (15 bp):
TCAATATCAACCAAT
Done.