Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014824.1 Kokia drynarioides strain JFW-HI SEQ_129866, 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: 44420
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:5879 original size:16 final size:16
Alignment explanation
Indices: 5858--5889 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5848 AATTTTAAAA
5858 TTTAAAAAATAAAGAT
1 TTTAAAAAATAAAGAT
*
5874 TTTAAATAATAAAGAT
1 TTTAAAAAATAAAGAT
5890 ATGAAGATAT
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:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
TTTAAAAAATAAAGAT
Found at i:6402 original size:41 final size:41
Alignment explanation
Indices: 6345--6426 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
6335 GCTTGAGAAA
6345 ATTCCTTTTTTCTCTTTGATTCCTGGTCAGTCCTTTCTTTT
1 ATTCCTTTTTTCTCTTTGATTCCTGGTCAGTCCTTTCTTTT
*
6386 ATTCCTTTTTTCTCTTTGATTCTTGGTCAGTCCTTTCTTTT
1 ATTCCTTTTTTCTCTTTGATTCCTGGTCAGTCCTTTCTTTT
6427 CTTTTTCCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.07, C:0.23, G:0.10, T:0.60
Consensus pattern (41 bp):
ATTCCTTTTTTCTCTTTGATTCCTGGTCAGTCCTTTCTTTT
Found at i:16184 original size:19 final size:20
Alignment explanation
Indices: 16146--16185 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16136 GAAAATTTTA
* *
16146 TTTTAATTTTATTTATACAT
1 TTTTAATATTATTTACACAT
16166 TTTTAATATTA-TTACACAT
1 TTTTAATATTATTTACACAT
16185 T
1 T
16186 GTTTTTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAATATTATTTACACAT
Found at i:16371 original size:93 final size:93
Alignment explanation
Indices: 16212--16399 Score: 349
Period size: 93 Copynumber: 2.0 Consensus size: 93
16202 TTTGTATATC
16212 TAAACTTACTATTATTTAAATCATTAAACGATTTGGTGTCACGTGTCAACCGAACACTAACATGA
1 TAAACTTACTATTATTTAAATCATTAAACGATTTGGTGTCACGTGTCAACCGAACACTAACATGA
16277 TCGAAGAAATTACTAAAATGCACTTTCA
66 TCGAAGAAATTACTAAAATGCACTTTCA
* *
16305 TAAACTTACTATTATTTAAATCATTGAATGATTTGGTGTCACGTGTCAACCGAACACTAACATGA
1 TAAACTTACTATTATTTAAATCATTAAACGATTTGGTGTCACGTGTCAACCGAACACTAACATGA
*
16370 TCGAAGAAATTATTAAAATGCACTTTCA
66 TCGAAGAAATTACTAAAATGCACTTTCA
16398 TA
1 TA
16400 TATAAAATAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (93 bp):
TAAACTTACTATTATTTAAATCATTAAACGATTTGGTGTCACGTGTCAACCGAACACTAACATGA
TCGAAGAAATTACTAAAATGCACTTTCA
Found at i:30381 original size:2 final size:2
Alignment explanation
Indices: 30374--30402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30364 CCCAGAACTA
30374 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
30403 TAAGAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:32265 original size:21 final size:21
Alignment explanation
Indices: 32240--32290 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
32230 TTTTTGAAGT
32240 TTTATATTTGAATTTATAAAC
1 TTTATATTTGAATTTATAAAC
* * * *
32261 TTTATGTTTGGATTTCTAAAT
1 TTTATATTTGAATTTATAAAC
32282 TTTATATTT
1 TTTATATTT
32291 CGATTGTGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.59
Consensus pattern (21 bp):
TTTATATTTGAATTTATAAAC
Found at i:32295 original size:21 final size:20
Alignment explanation
Indices: 32239--32295 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
32229 TTTTTTGAAG
32239 TTTTATATTTGAATTTATAAA
1 TTTTATATTTG-ATTTATAAA
* * *
32260 CTTTATGTTTGGATTTCTAAA
1 TTTTATATTT-GATTTATAAA
32281 TTTTATATTTCGATT
1 TTTTATATTT-GATT
32296 GTGCTATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTTATATTTGATTTATAAA
Found at i:32420 original size:16 final size:16
Alignment explanation
Indices: 32399--32434 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
32389 GTACCCTATG
32399 ACCCAAAAATACGAGT
1 ACCCAAAAATACGAGT
* *
32415 ACCCAAAATTCCGAGT
1 ACCCAAAAATACGAGT
32431 ACCC
1 ACCC
32435 GATTTGTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (16 bp):
ACCCAAAAATACGAGT
Found at i:36620 original size:15 final size:15
Alignment explanation
Indices: 36600--36650 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
36590 ACAAAACGAT
36600 AACGTAAATGATTAA
1 AACGTAAATGATTAA
*
36615 AACGTAACAT--TTCA
1 AACGTAA-ATGATTAA
*
36629 AACATAAATGATTAA
1 AACGTAAATGATTAA
*
36644 AATGTAA
1 AACGTAA
36651 TCTAAAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (15 bp):
AACGTAAATGATTAA
Found at i:38584 original size:32 final size:29
Alignment explanation
Indices: 38547--38610 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 29
38537 TTAAATTAGC
*
38547 TTTTTAAAATTTAAAAAGAATTATAAAAATTA
1 TTTTTAAAAATTAAAAA-AATT-TAAAAA-TA
*
38579 TTTTTAAAAATTAAAAATATTTAAAAATA
1 TTTTTAAAAATTAAAAAAATTTAAAAATA
38608 TTT
1 TTT
38611 AAAAATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 6 0.20
31 3 0.10
32 16 0.53
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
TTTTTAAAAATTAAAAAAATTTAAAAATA
Found at i:38593 original size:20 final size:21
Alignment explanation
Indices: 38556--38621 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
38546 CTTTTTAAAA
*
38556 TTTAAAAAGAATTATAAAAATTAT
1 TTTAAAAA-TATT-TAAAAA-TAT
*
38580 TTTTAAAA-A-TTAAAAATA-
1 TTTAAAAATATTTAAAAATAT
38598 TTTAAAAATATTTAAAAATAT
1 TTTAAAAATATTTAAAAATAT
38619 TTT
1 TTT
38622 CTTAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 7 0.19
19 3 0.08
20 15 0.41
21 4 0.11
22 1 0.03
24 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAAAAATATTTAAAAATAT
Found at i:38604 original size:10 final size:10
Alignment explanation
Indices: 38589--38620 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
38579 TTTTTAAAAA
38589 TTAAAAATAT
1 TTAAAAATAT
38599 TTAAAAATAT
1 TTAAAAATAT
38609 TTAAAAATAT
1 TTAAAAATAT
38619 TT
1 TT
38621 TCTTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:41094 original size:13 final size:14
Alignment explanation
Indices: 41076--41108 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
41066 ATGTAAGACT
41076 TTTTTTG-AAAACA
1 TTTTTTGCAAAACA
41089 TTTTTTGCAAAACA
1 TTTTTTGCAAAACA
41103 TTTTTT
1 TTTTTT
41109 TAATACATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTTTTGCAAAACA
Found at i:41094 original size:14 final size:15
Alignment explanation
Indices: 41075--41109 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
41065 CATGTAAGAC
41075 TTTTTTTG-AAAACA
1 TTTTTTTGCAAAACA
41089 -TTTTTTGCAAAACA
1 TTTTTTTGCAAAACA
41103 TTTTTTT
1 TTTTTTT
41110 AATACATCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
15 6 0.32
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTTTTTGCAAAACA
Done.