Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010016.1 Kokia drynarioides strain JFW-HI SEQ_124779, 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: 3887
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.37
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:766 original size:20 final size:21
Alignment explanation
Indices: 727--765 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
717 TATGAGATAA
727 ATAATAATTATAAAATAAAAC
1 ATAATAATTATAAAATAAAAC
748 ATAAT-ATTAT-AAATAAAA
1 ATAATAATTATAAAATAAAA
766 AATATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATAATTATAAAATAAAAC
Found at i:767 original size:21 final size:20
Alignment explanation
Indices: 727--767 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
717 TATGAGATAA
*
727 ATAATAATTATAAAATAAAAC
1 ATAAT-ATTATAAAAAAAAAC
748 ATAATATTATAAATAAAAAA
1 ATAATATTATAAA-AAAAAA
768 TATACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAATATTATAAAAAAAAAC
Found at i:1662 original size:22 final size:22
Alignment explanation
Indices: 1634--1692 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1624 GTTGTTTTGG
1634 TTTTTTTTACTGTTTTGGTTGA-
1 TTTTTTTTACTGTTTT-GTTGAC
*
1656 TTTTTTTTGCTG-TTT-TTGAC
1 TTTTTTTTACTGTTTTGTTGAC
*
1676 TTTTTTTTATTGTTTTG
1 TTTTTTTTACTGTTTTG
1693 ATTGCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 6 0.19
22 11 0.35
ACGTcount: A:0.07, C:0.05, G:0.15, T:0.73
Consensus pattern (22 bp):
TTTTTTTTACTGTTTTGTTGAC
Found at i:1689 original size:20 final size:19
Alignment explanation
Indices: 1628--1695 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 19
1618 TATATTGTTG
*
1628 TTTTGGTTTTTTTTACTGTT
1 TTTTGATTTTTTTTACTG-T
*
1648 TTGGTTGATTTTTTTTGCTGT
1 TT--TTGATTTTTTTTACTGT
*
1669 TTTTGACTTTTTTTTATTG-
1 TTTTGA-TTTTTTTTACTGT
1688 TTTTGATT
1 TTTTGATT
1696 GCTATTTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.05
19 10 0.24
20 12 0.29
21 3 0.07
22 14 0.34
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.72
Consensus pattern (19 bp):
TTTTGATTTTTTTTACTGT
Found at i:1765 original size:24 final size:23
Alignment explanation
Indices: 1711--1765 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1701 TTTCATGTTA
1711 TTTTTGTTGTTTTACTGTTATTT
1 TTTTTGTTGTTTTACTGTTATTT
** **
1734 TTGCTGTTGTTTTTGTTGTTATTT
1 TTTTTGTTG-TTTTACTGTTATTT
1758 TTTTTGTT
1 TTTTTGTT
1766 TGGATGTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.05, C:0.04, G:0.16, T:0.75
Consensus pattern (23 bp):
TTTTTGTTGTTTTACTGTTATTT
Found at i:2248 original size:22 final size:22
Alignment explanation
Indices: 2220--2278 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2210 GTTGTTTTGG
2220 TTTTTTTTACTGTTTTGGTTGA-
1 TTTTTTTTACTGTTTT-GTTGAC
*
2242 TTTTTTTTGCTG-TTT-TTGAC
1 TTTTTTTTACTGTTTTGTTGAC
*
2262 TTTTTTTTATTGTTTTG
1 TTTTTTTTACTGTTTTG
2279 ATTGCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 6 0.19
22 11 0.35
ACGTcount: A:0.07, C:0.05, G:0.15, T:0.73
Consensus pattern (22 bp):
TTTTTTTTACTGTTTTGTTGAC
Found at i:2275 original size:20 final size:19
Alignment explanation
Indices: 2214--2281 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 19
2204 TATATTGTTG
*
2214 TTTTGGTTTTTTTTACTGTT
1 TTTTGATTTTTTTTACTG-T
*
2234 TTGGTTGATTTTTTTTGCTGT
1 TT--TTGATTTTTTTTACTGT
*
2255 TTTTGACTTTTTTTTATTG-
1 TTTTGA-TTTTTTTTACTGT
2274 TTTTGATT
1 TTTTGATT
2282 GCTATTTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.05
19 10 0.24
20 12 0.29
21 3 0.07
22 14 0.34
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.72
Consensus pattern (19 bp):
TTTTGATTTTTTTTACTGT
Found at i:2309 original size:20 final size:20
Alignment explanation
Indices: 2286--2364 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
2276 TTGATTGCTA
*
2286 TTTTCATGTTATTTTTGTTG
1 TTTTGATGTTATTTTTGTTG
2306 TTTT-ACTGTTATTTTTGCTACTG
1 TTTTGA-TGTTATTTTTG-T--TG
* *
2329 TTTTTGTTGTTATTTTTTTTG
1 -TTTTGATGTTATTTTTGTTG
*
2350 TTTGGATGTTATTTT
1 TTTTGATGTTATTTT
2365 ATATGCATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
19 1 0.02
20 28 0.57
21 3 0.06
23 3 0.06
24 14 0.29
ACGTcount: A:0.10, C:0.05, G:0.15, T:0.70
Consensus pattern (20 bp):
TTTTGATGTTATTTTTGTTG
Found at i:3302 original size:27 final size:26
Alignment explanation
Indices: 3287--3343 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 26
3277 ATAATTTTCA
3287 TAATAAACATGAATTTAATAAATAATT
1 TAATAAACATGAATTTAAT-AATAATT
3314 TAATAAACATGAATTTAATAAATAATT
1 TAATAAACATGAATTTAAT-AATAATT
3341 TAA
1 TAA
3344 AAAATGGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (26 bp):
TAATAAACATGAATTTAATAATAATT
Found at i:3307 original size:15 final size:15
Alignment explanation
Indices: 3287--3335 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
3277 ATAATTTTCA
3287 TAATAAACATGAATT
1 TAATAAACATGAATT
3302 TAAT-AA-AT-AATT
1 TAATAAACATGAATT
3314 TAATAAACATGAATT
1 TAATAAACATGAATT
3329 TAATAAA
1 TAATAAA
3336 TAATTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.26
13 4 0.13
14 4 0.13
15 15 0.48
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (15 bp):
TAATAAACATGAATT
Found at i:3315 original size:12 final size:12
Alignment explanation
Indices: 3298--3348 Score: 66
Period size: 12 Copynumber: 4.0 Consensus size: 12
3288 AATAAACATG
3298 AATTTAATAAAT
1 AATTTAATAAAT
3310 AATTTAATAAACAT
1 AATTTAAT-AA-AT
3324 GAATTTAATAAAT
1 -AATTTAATAAAT
*
3337 AATTTAAAAAAT
1 AATTTAATAAAT
3349 GGGAGGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
12 19 0.54
13 4 0.11
14 4 0.11
15 8 0.23
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (12 bp):
AATTTAATAAAT
Found at i:3482 original size:6 final size:6
Alignment explanation
Indices: 3471--3495 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3461 AACATATACC
3471 AAACCA AAACCA AAACCA AAACCA A
1 AAACCA AAACCA AAACCA AAACCA A
3496 CAATTCTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCA
Found at i:3540 original size:59 final size:61
Alignment explanation
Indices: 3445--3570 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 61
3435 AGCCAAAAAT
3445 GAGACACACCGAATACAACATATACCAAACCAAAACCAAAACCAAAACCAACAATTCTCCAAACA
1 GAGACACACCGAATACAACATAT----AACCAAAACCAAAACCAAAACCAACAATTCTCCAAACA
*
3510 GAGACACACCGAATACAGCATAT-ACC-AAACCAAAACCAAAACCAACAATTCTCCAAACA
1 GAGACACACCGAATACAACATATAACCAAAACCAAAACCAAAACCAACAATTCTCCAAACA
3569 GA
1 GA
3571 TTACCGATAT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
59 35 0.58
60 3 0.05
65 22 0.37
ACGTcount: A:0.52, C:0.32, G:0.06, T:0.10
Consensus pattern (61 bp):
GAGACACACCGAATACAACATATAACCAAAACCAAAACCAAAACCAACAATTCTCCAAACA
Done.