Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168447.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_659, 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: 20412
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:225 original size:26 final size:26
Alignment explanation
Indices: 191--246 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
181 CATTAAATGA
* * *
191 AAATTTTTTTAAATTTAAAAAATTTG
1 AAATGTTTTAAAAATTAAAAAATTTG
*
217 AAATGTTTTAAAAATTAAAAAATTTT
1 AAATGTTTTAAAAATTAAAAAATTTG
243 AAAT
1 AAAT
247 ATATGAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
AAATGTTTTAAAAATTAAAAAATTTG
Found at i:718 original size:21 final size:21
Alignment explanation
Indices: 660--719 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
650 ATAATTAAAA
* *
660 AAAAAGTTTTTATAATTTTTT
1 AAAAATTTTTTATATTTTTTT
*
681 AAAAATTTTTTAGATTTTTTT
1 AAAAATTTTTTATATTTTTTT
* *
702 GAAAATTTTTTTTATTTT
1 AAAAATTTTTTATATTTT
720 CAAATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
AAAAATTTTTTATATTTTTTT
Found at i:783 original size:18 final size:18
Alignment explanation
Indices: 762--800 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
752 ATTGATGAAA
762 TTTTA-TTTGTATTAAAAT
1 TTTTATTTTGT-TTAAAAT
780 TTTTATTTTGTTTAAAAT
1 TTTTATTTTGTTTAAAAT
798 TTT
1 TTT
801 CATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTATTTTGTTTAAAAT
Found at i:916 original size:20 final size:19
Alignment explanation
Indices: 870--934 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
860 GTATTTTCAT
870 AAAATTTA-AATTATTTAAA
1 AAAATTTATAATT-TTTAAA
** *
889 TTATTTTATAATTTTTAAA
1 AAAATTTATAATTTTTAAA
*
908 AAATATTTATATTTTTTAAA
1 AAA-ATTTATAATTTTTAAA
928 AAAATTT
1 AAAATTT
935 TAAAAATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAATTTATAATTTTTAAA
Found at i:944 original size:20 final size:21
Alignment explanation
Indices: 898--944 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
888 ATTATTTTAT
* *
898 AATTTTTAAAAAATATTTATA
1 AATTTTAAAAAAATATTTAAA
**
919 TTTTTTAAAAAAAT-TTTAAA
1 AATTTTAAAAAAATATTTAAA
939 AATTTT
1 AATTTT
945 TGAATGTTTG
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTAAAAAAATATTTAAA
Found at i:1275 original size:20 final size:20
Alignment explanation
Indices: 1247--1292 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1237 GAAATGTTTT
1247 AAAATTTTTTA-AAAATAT-
1 AAAATTTTTTAGAAAATATA
*
1265 AAAATATTTTTAGAAATTATA
1 AAAAT-TTTTTAGAAAATATA
1286 AAAATTT
1 AAAATTT
1293 AAACATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 8 0.33
21 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTTTTTAGAAAATATA
Found at i:1276 original size:19 final size:20
Alignment explanation
Indices: 1246--1292 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1236 TGAAATGTTT
1246 TAAAAT-TTTTTA-AAAATA
1 TAAAATATTTTTAGAAAATA
*
1264 TAAAATATTTTTAGAAATTA
1 TAAAATATTTTTAGAAAATA
1284 TAAAA-ATTT
1 TAAAATATTT
1293 AAACATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 10 0.38
20 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAAATATTTTTAGAAAATA
Found at i:1482 original size:37 final size:37
Alignment explanation
Indices: 1401--1490 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
1391 AAAAAGGATT
*
1401 AAAAATTTTTAAAAAATTAATAATCTAAAATTTTTTGA
1 AAAAATTTTTAAAAAA-TAAAAATCTAAAATTTTTTGA
* *
1439 ATAAAATTTTTAAATTAAA-AAAAATCT-AATTTTTTTTA
1 A-AAAATTTTTAAA--AAATAAAAATCTAAAATTTTTTGA
*
1477 AAAAATTTTGAAAA
1 AAAAATTTTTAAAA
1491 TTTATAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
35 1 0.02
37 11 0.24
38 11 0.24
39 19 0.42
41 3 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (37 bp):
AAAAATTTTTAAAAAATAAAAATCTAAAATTTTTTGA
Found at i:1859 original size:23 final size:22
Alignment explanation
Indices: 1815--1860 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1805 AATTTTTTCA
*
1815 ATTTTTTAAAATTTTTTATTTT
1 ATTTTTTAAAATTTTATATTTT
*
1837 ATTTTTGTAAAATTTTATGTTTT
1 ATTTTT-TAAAATTTTATATTTT
1860 A
1 A
1861 AAATTTTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTTTAAAATTTTATATTTT
Found at i:1864 original size:15 final size:15
Alignment explanation
Indices: 1832--1882 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1822 AAAATTTTTT
*
1832 ATTTTATTTTTGTAAA
1 ATTTTATGTTT-TAAA
1848 ATTTTATGTTTTAAA
1 ATTTTATGTTTTAAA
* **
1863 ATTTTGTGAATTAAA
1 ATTTTATGTTTTAAA
1878 ATTTT
1 ATTTT
1883 TTTTAATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 21 0.68
16 10 0.32
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (15 bp):
ATTTTATGTTTTAAA
Found at i:2541 original size:14 final size:13
Alignment explanation
Indices: 2517--2555 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2507 TTAAAATTTT
2517 TATTTTT-ATATA
1 TATTTTTAATATA
2529 TATTTTTTAATATA
1 TA-TTTTTAATATA
2543 -ATTTTTAATATA
1 TATTTTTAATATA
2555 T
1 T
2556 TTAAGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 13 0.54
13 6 0.25
14 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTAATATA
Found at i:14202 original size:23 final size:23
Alignment explanation
Indices: 14175--14232 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
14165 AAATAATAAT
14175 AAAATTATTATAATTACAATTAA
1 AAAATTATTATAATTACAATTAA
*
14198 AAAATTATTATAATTATAATTAA
1 AAAATTATTATAATTACAATTAA
14221 AAAA-TATT-TAAT
1 AAAATTATTATAAT
14233 AAAAAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 26 0.76
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATTATTATAATTACAATTAA
Found at i:14232 original size:15 final size:17
Alignment explanation
Indices: 14214--14250 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
14204 ATTATAATTA
14214 TAATTAAAAAA-TAT-T
1 TAATTAAAAAATTATAT
*
14229 TAATAAAAAAATTATAT
1 TAATTAAAAAATTATAT
14246 TAATT
1 TAATT
14251 TAGTCTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.56
16 3 0.17
17 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAAAAAATTATAT
Found at i:15298 original size:18 final size:18
Alignment explanation
Indices: 15277--15313 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
15267 CTGTCTTTTA
15277 TTGACTTAGAAAGGTGTT
1 TTGACTTAGAAAGGTGTT
15295 TTGACTTAGAAAGGTGTT
1 TTGACTTAGAAAGGTGTT
15313 T
1 T
15314 GGGAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (18 bp):
TTGACTTAGAAAGGTGTT
Found at i:17001 original size:2 final size:2
Alignment explanation
Indices: 16991--17026 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
16981 TTTTTCTTGC
16991 AT AT A- AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17027 CCATAGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19600 original size:3 final size:3
Alignment explanation
Indices: 19592--19620 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19582 AAGTTTGCCT
19592 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19621 TTGTGCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.