Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168045.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_297, 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: 37297
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:336 original size:178 final size:178
Alignment explanation
Indices: 6--337 Score: 388
Period size: 178 Copynumber: 1.9 Consensus size: 178
1 AATTC
* * *
6 AAATAGTTATGACTATTTAAACAATTATTTATCTCAAATCATTATGATTTTTGTTTGTCATAAAA
1 AAATAGTTAAGACTATTTAAACAATTATCTATCTCAAATCATTATGACTTTTGTTTGTCATAAAA
* * * * * **
71 AAATTGTTTCTGTTTATACAAGCTTATTTGAGTAAAATATTGCTAAAATAATAATATTTTAAAAA
66 AAATTGTTTCTGTTCATACAAGCTTATTTGAATAAAATAATACTAAAATAATAACATTCAAAAAA
*
136 TTAATAACTAAGAGATTTAAAAAATAAATATGTTTGCAGAACTAGTTT
131 TTAATAACTAAGAGAATTAAAAAATAAATATGTTTGCAGAACTAGTTT
* * *
184 AAATAGTTAAGA-TATTTGAACAATT-TCTATTTCAAATCGTTATGACCTTTTGTTTAGTCATAA
1 AAATAGTTAAGACTATTTAAACAATTATCTATCTCAAATCATTATGA-CTTTTGTTT-GTCATAA
* * *** *
247 AATAATTGTTT-TAGTTCATATATA-CTTATTTGAAATAAAATAATACTATTTTATTAACATTCA
64 AAAAATTGTTTCT-GTTCATACA-AGCTTATTTG-AATAAAATAATACTAAAATAATAACATTCA
310 AAAAATTAATAAGC-AAGA-AATTAAAAAA
126 AAAAATTAATAA-CTAAGAGAATTAAAAAA
338 AATCTATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
176 17 0.13
177 21 0.16
178 52 0.41
179 37 0.29
180 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (178 bp):
AAATAGTTAAGACTATTTAAACAATTATCTATCTCAAATCATTATGACTTTTGTTTGTCATAAAA
AAATTGTTTCTGTTCATACAAGCTTATTTGAATAAAATAATACTAAAATAATAACATTCAAAAAA
TTAATAACTAAGAGAATTAAAAAATAAATATGTTTGCAGAACTAGTTT
Found at i:3105 original size:18 final size:18
Alignment explanation
Indices: 3082--3133 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
3072 AATAAGTTTA
3082 AATAGTTATGACTATTTG
1 AATAGTTATGACTATTTG
*
3100 AATAGTTAT-A-TAATTTA
1 AATAGTTATGACT-ATTTG
*
3117 AATCGTTATGACT-TTTG
1 AATAGTTATGACTATTTG
3134 TTTTGTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.04
17 16 0.57
18 10 0.36
19 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (18 bp):
AATAGTTATGACTATTTG
Found at i:3456 original size:144 final size:143
Alignment explanation
Indices: 3273--3564 Score: 385
Period size: 144 Copynumber: 2.0 Consensus size: 143
3263 AAACAATTGG
* * *
3273 TTTATGACAAAACAAAATGTCATAGCTATTTGAAATAGATAATTGTTCAAATAGTTATAACTATT
1 TTTATGACAAAACAAAAGGTCATAGATATTTGAAATAGATAATTGTTCAAATAATTATAACTATT
* * * * *
3338 TGAA-TGTGTTCAGAAAAATAGATTTATTTTTTAAATTTC-TACTTAGTAATTTTTGAAATATTA
66 TGAACT-TGTAC-GAAAAATAGATTCATTTTTTAAATCTCTTACTCAGTAATTTTAGAAATATTA
3401 ATAAATTTA-TATTAT
129 ATAAA-TTAGTATTAT
* *
3416 TTTATGACAAAAACAAAAGGTCTTA-ATGATTTGAAATAGATAATTGTTCAATTAATTATAACTA
1 TTTATGAC-AAAACAAAAGGTCATAGAT-ATTTGAAATAGATAATTGTTCAAATAATTATAACTA
** * *
3480 TTTGAACTTGTACGGTAAATAGATTCATTTTTTAAATCTCTTACTCATTAATTTTAGGAATATTA
64 TTTGAACTTGTACGAAAAATAGATTCATTTTTTAAATCTCTTACTCAGTAATTTTAGAAATATTA
3545 ATAAATTAGTATTAT
129 ATAAATTAGTATTAT
3560 TTTAT
1 TTTAT
3565 TTTGAATAAG
Statistics
Matches: 130, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
143 35 0.27
144 94 0.72
145 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (143 bp):
TTTATGACAAAACAAAAGGTCATAGATATTTGAAATAGATAATTGTTCAAATAATTATAACTATT
TGAACTTGTACGAAAAATAGATTCATTTTTTAAATCTCTTACTCAGTAATTTTAGAAATATTAAT
AAATTAGTATTAT
Found at i:11017 original size:21 final size:21
Alignment explanation
Indices: 10982--11023 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10972 TTGGTGGTTG
* *
10982 TGAAGCGAGGGAGGGATGAAT
1 TGAAGCGACGAAGGGATGAAT
*
11003 TGAAGCGACGAAGGGCTGAAT
1 TGAAGCGACGAAGGGATGAAT
11024 CTTAGTGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.43, T:0.14
Consensus pattern (21 bp):
TGAAGCGACGAAGGGATGAAT
Found at i:13692 original size:30 final size:30
Alignment explanation
Indices: 13656--13715 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
13646 TAGGTTGACC
13656 CTAGGAGCACATGTGGGCTGACACACATCT
1 CTAGGAGCACATGTGGGCTGACACACATCT
13686 CTAGGAGCACATGTGGGCTGACACACATCT
1 CTAGGAGCACATGTGGGCTGACACACATCT
13716 AGATGGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (30 bp):
CTAGGAGCACATGTGGGCTGACACACATCT
Found at i:19028 original size:67 final size:68
Alignment explanation
Indices: 18917--19051 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 68
18907 AGTTTAAGAT
*
18917 AGGTCAAGGGTGTTGTGGCCCCTGATGCCTCTAATCATTAGCTTTACCTGATGGAATTCACCAAG
1 AGGTCAAGGGTGTTGTGGCCCCTAATGCCTCTAATCATTAGCTTTACCTGATGGAATTCACCAAG
18982 GGC
66 GGC
* * *
18985 AGGTCGAGGGTGTTGTGGCCCC-AATGCCTCTAATCATTAGCTTTACTTGATGGAATTCACTAAG
1 AGGTCAAGGGTGTTGTGGCCCCTAATGCCTCTAATCATTAGCTTTACCTGATGGAATTCACCAAG
19049 GGC
66 GGC
19052 TCCAACTATC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 42 0.67
68 21 0.33
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (68 bp):
AGGTCAAGGGTGTTGTGGCCCCTAATGCCTCTAATCATTAGCTTTACCTGATGGAATTCACCAAG
GGC
Found at i:34534 original size:44 final size:45
Alignment explanation
Indices: 34441--34534 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
34431 ATTGAGGCAT
* * * *
34441 GTGCCTACACTAAGGGCTAGCATGTGCTAATGGTGGTTGAGACAA
1 GTGCCTACACCAAGGGCTAGCATGTGCCAATGGCGGTTAAGACAA
* * **
34486 GTGCCTATACCAAGGGCTAGCTTGT-CCAATGGCGGTTAAGGTAA
1 GTGCCTACACCAAGGGCTAGCATGTGCCAATGGCGGTTAAGACAA
34530 GTGCC
1 GTGCC
34535 CTCGATAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
GTGCCTACACCAAGGGCTAGCATGTGCCAATGGCGGTTAAGACAA
Done.