Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006532.1 Kokia drynarioides strain JFW-HI SEQ_121116, 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: 18053
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:817 original size:53 final size:53
Alignment explanation
Indices: 737--843 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
727 TGCTCCTAAG
737 CTAGCTTGTGGAGACAAAAAAAGGTCCAATCTTTCCCTGACCAAACCATGGCC
1 CTAGCTTGTGGAGACAAAAAAAGGTCCAATCTTTCCCTGACCAAACCATGGCC
*
790 CTAGCTTGTGGAGACAAAAAAAGGTCCAATCTTTCCCTGACCGAACCATGGCC
1 CTAGCTTGTGGAGACAAAAAAAGGTCCAATCTTTCCCTGACCAAACCATGGCC
843 C
1 C
844 CTCCTATTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (53 bp):
CTAGCTTGTGGAGACAAAAAAAGGTCCAATCTTTCCCTGACCAAACCATGGCC
Found at i:2025 original size:2 final size:2
Alignment explanation
Indices: 2018--2064 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2008 ATAAACGCAA
*
2018 AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2060 AG AG A
1 AG AG A
2065 ACAAATTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3308 original size:14 final size:15
Alignment explanation
Indices: 3289--3323 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3279 TATACGAATG
*
3289 AATAAATATATG-AA
1 AATAAATATAAGAAA
3303 AATAAATATAAGAAA
1 AATAAATATAAGAAA
3318 AATAAA
1 AATAAA
3324 ATACGAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AATAAATATAAGAAA
Found at i:3508 original size:28 final size:29
Alignment explanation
Indices: 3452--3698 Score: 155
Period size: 29 Copynumber: 8.6 Consensus size: 29
3442 TAGAGAGTTC
* * *
3452 GGGTTAAAACGTAATTTTGGAAAGTTTAG
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
3481 GGGTAAAAATGTAATTTTGGGAAG-TTA-
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
***
3508 GGG-AAAAATGTAATTTTTAAAAGTTTAG
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
* * * *
3536 GAGCAAAAATGTAATTTTTGAGAAGTTCA-
1 GGGTAAAAATGTAA-TTTTGGGAAGTTTAG
* * *
3565 GGGTAAAAATATGATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
* * * * *
3594 GGG-CAAAATATAATTTTTGAGAAATTTAA
1 GGGTAAAAATGTAA-TTTTGGGAAGTTTAG
* * * *
3623 GGGTAAAAATATGATTTTTGGAAGTTTTG
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
* * ** * * *
3652 TGGCAAAAACATAATTTTTGGAA-ATTCG
1 GGGTAAAAATGTAATTTTGGGAAGTTTAG
*
3680 AGGGAAAAAATGTAATTTT
1 -GGGTAAAAATGTAATTTT
3699 TAAAGAAAAT
Statistics
Matches: 170, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
26 17 0.10
27 6 0.04
28 27 0.16
29 101 0.59
30 19 0.11
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTGGGAAGTTTAG
Found at i:3591 original size:58 final size:58
Alignment explanation
Indices: 3466--3699 Score: 244
Period size: 58 Copynumber: 4.1 Consensus size: 58
3456 TAAAACGTAA
* * * *
3466 TTTTGGAAAGTTTAGGGGTAAAAATGTAA-TTTTGGGAAGTT-AGGG-AAAAATGTAAT
1 TTTTGG-AAGTTTAGGGGCAAAAATATAATTTTTGAGAAGTTCAGGGTAAAAATATAAT
** * * *
3522 TTTTAAAAGTTTAGGAGCAAAAATGTAATTTTTGAGAAGTTCAGGGTAAAAATATGAT
1 TTTTGGAAGTTTAGGGGCAAAAATATAATTTTTGAGAAGTTCAGGGTAAAAATATAAT
* * *
3580 TTTTGGAAGTTTAGGGGC-AAAATATAATTTTTGAGAAATTTAAGGGTAAAAATATGAT
1 TTTTGGAAGTTTAGGGGCAAAAATATAATTTTTGAG-AAGTTCAGGGTAAAAATATAAT
* * * * * *
3638 TTTTGGAAGTTTTGTGGCAAAAACATAATTTTTG-GAAATTCGAGGGAAAAAATGTAAT
1 TTTTGGAAGTTTAGGGGCAAAAATATAATTTTTGAGAAGTTC-AGGGTAAAAATATAAT
3696 TTTT
1 TTTT
3700 AAAGAAAATA
Statistics
Matches: 151, Mismatches: 21, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
55 20 0.13
56 15 0.10
57 24 0.16
58 78 0.52
59 14 0.09
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (58 bp):
TTTTGGAAGTTTAGGGGCAAAAATATAATTTTTGAGAAGTTCAGGGTAAAAATATAAT
Found at i:6343 original size:59 final size:59
Alignment explanation
Indices: 6269--6456 Score: 245
Period size: 59 Copynumber: 3.2 Consensus size: 59
6259 AATCAGGAAT
*
6269 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAA
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTCGAGAA
* *
6328 TCTGGGATAACTTTCAAACATCCCGAGAAT-CTGGGATAACTTTCAAGCATC-CTGAGAA
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTC-GAGAA
* * * * * *
6386 TCTCGAGATAACTTTCAATCATCTCGAGAATCTCGGGATAATTTTCAAACATCTTGAGAA
1 TCT-GGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTCGAGAA
*
6446 TCCGAGGATAA
1 TCTG-GGATAA
6457 TTTTTAGATT
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 26 0.23
59 55 0.50
60 29 0.26
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (59 bp):
TCTGGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTCGAGAA
Found at i:6418 original size:88 final size:89
Alignment explanation
Indices: 6269--6456 Score: 288
Period size: 88 Copynumber: 2.1 Consensus size: 89
6259 AATCAGGAAT
6269 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCT-GG
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCTCGG
6333 GATAACTTTCAAACATCCCGAGAA
66 GATAACTTTCAAACATCCCGAGAA
* * * *
6357 TCTGGGATAACTTTCAAGCATCCTGAGAATCTCGAGATAACTTTCAATCATCTCGAGAATCTCGG
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCTCGG
* **
6422 GATAATTTTCAAACATCTTGAGAA
66 GATAACTTTCAAACATCCCGAGAA
*
6446 TCCGAGGATAA
1 TCTG-GGATAA
6457 TTTTTAGATT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 58 0.64
89 26 0.29
90 6 0.07
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (89 bp):
TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCTCGG
GATAACTTTCAAACATCCCGAGAA
Found at i:6460 original size:30 final size:29
Alignment explanation
Indices: 6272--6456 Score: 226
Period size: 30 Copynumber: 6.2 Consensus size: 29
6262 CAGGAATTCT
6272 GGGATAACTTTCAAACATCCCGAGAATCCC
1 GGGATAACTTTCAAACATCCCGAGAAT-CC
* * *
6302 GAGATAACTTTCAAACATCTCGAGAATCT
1 GGGATAACTTTCAAACATCCCGAGAATCC
*
6331 GGGATAACTTTCAAACATCCCGAGAATCT
1 GGGATAACTTTCAAACATCCCGAGAATCC
* *
6360 GGGATAACTTTCAAGCATCCTGAGAATCTC
1 GGGATAACTTTCAAACATCCCGAGAATC-C
* * *
6390 GAGATAACTTTCAATCATCTCGAGAATCTC
1 GGGATAACTTTCAAACATCCCGAGAATC-C
* **
6420 GGGATAATTTTCAAACATCTTGAGAATCC
1 GGGATAACTTTCAAACATCCCGAGAATCC
6449 GAGGATAA
1 G-GGATAA
6457 TTTTTAGATT
Statistics
Matches: 137, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
29 56 0.41
30 81 0.59
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (29 bp):
GGGATAACTTTCAAACATCCCGAGAATCC
Found at i:6864 original size:49 final size:46
Alignment explanation
Indices: 6759--6875 Score: 126
Period size: 49 Copynumber: 2.4 Consensus size: 46
6749 AACTCGAGCT
* * *
6759 CTAGTTCACGGTGATTATACGATCACGGGTTGAAGTATAACTAGAG
1 CTAGTTGACGGTGGTTATGCGATCACGGGTTGAAGTATAACTAGAG
* *
6805 CTATCGGTTGACGGTGGTTATGCGATCACGGGTTGGAGTATAACTTGGAAG
1 CTA---GTTGACGGTGGTTATGCGATCACGGGTTGAAGTATAAC-TAG-AG
*
6856 CCTAGTTGACAGTGGTTATG
1 -CTAGTTGACGGTGGTTATG
6876 TGGTCACGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
46 3 0.05
49 49 0.83
50 2 0.03
51 2 0.03
52 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.30
Consensus pattern (46 bp):
CTAGTTGACGGTGGTTATGCGATCACGGGTTGAAGTATAACTAGAG
Done.