Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168440.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_652, 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: 20561
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Found at i:1343 original size:9 final size:9
Alignment explanation
Indices: 1329--1358 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1319 AATATTTTAT
1329 TAATTAAAA
1 TAATTAAAA
1338 TAATTAAAA
1 TAATTAAAA
1347 TATATTAAAA
1 TA-ATTAAAA
1357 TA
1 TA
1359 TAAAAATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:1355 original size:10 final size:10
Alignment explanation
Indices: 1331--1360 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1321 TATTTTATTA
1331 ATTAAAATA-
1 ATTAAAATAT
1340 ATTAAAATAT
1 ATTAAAATAT
1350 ATTAAAATAT
1 ATTAAAATAT
1360 A
1 A
1361 AAAATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:2135 original size:18 final size:19
Alignment explanation
Indices: 2091--2136 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2081 ATTAATTTGC
*
2091 TAATTTTAATGTATTAAAA
1 TAATTTTAATGTAATAAAA
*
2110 -AATGTTTACT-TAATAAAA
1 TAAT-TTTAATGTAATAAAA
2128 TAATTTTAA
1 TAATTTTAA
2137 AGATTGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TAATTTTAATGTAATAAAA
Found at i:3895 original size:15 final size:14
Alignment explanation
Indices: 3875--3905 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3865 ATCTAATTAT
3875 AAAATTATAATATAA
1 AAAATTATAA-ATAA
3890 AAAATTATAAATAA
1 AAAATTATAAATAA
3904 AA
1 AA
3906 TACTCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTATAAATAA
Found at i:4722 original size:14 final size:15
Alignment explanation
Indices: 4703--4738 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4693 GAAATTGAAT
4703 TGATAAAT-TTTTAG
1 TGATAAATCTTTTAG
*
4717 TGATAAATCTTTTGG
1 TGATAAATCTTTTAG
4732 TGATAAA
1 TGATAAA
4739 GTCATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (15 bp):
TGATAAATCTTTTAG
Found at i:4746 original size:55 final size:56
Alignment explanation
Indices: 4656--4783 Score: 170
Period size: 56 Copynumber: 2.3 Consensus size: 56
4646 TTTTCATTTA
* *
4656 TTTATTGATAAATTCTTTCGGTGATAAAGTCATTTTTGAA-ATTGAATTGATAAATT
1 TTTAGTGATAAA-TCTTTCGGTGATAAAGTCATTTTTGAAGATTGAATAGATAAATT
* * *
4712 TTTAGTGATAAATCTTTTGGTGATAAAGTCATTTTTTAAGTTTGAATAGATAAATT
1 TTTAGTGATAAATCTTTCGGTGATAAAGTCATTTTTGAAGATTGAATAGATAAATT
* *
4768 CTTGGTGATAAA-CTTT
1 TTTAGTGATAAATCTTT
4784 GGATAAAGTC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
55 29 0.45
56 35 0.55
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (56 bp):
TTTAGTGATAAATCTTTCGGTGATAAAGTCATTTTTGAAGATTGAATAGATAAATT
Found at i:11424 original size:353 final size:350
Alignment explanation
Indices: 10622--11770 Score: 1273
Period size: 353 Copynumber: 3.3 Consensus size: 350
10612 TGCAACCACA
* * * *
10622 TTCACTAATTATATACAAACTGTGATAGGAATTATTAAATGCATCTTTCTTAGATATATGCCTTT
1 TTCACTAATTATCTACAAACTGTGATAGAAATTATTAAATG-A-CTTTCTTAGATATACGCCTTC
** * * *
10687 AATAACCATG-TAAAATTTATGTGACGGTATATAGAACGTA-TTTACAGTAGAAGATACCTTTAG
64 AATAACTGTGTTAAAATTTATGTGACGGTATATAGAATGCATTTTACAGTAGAAGATACCTTTAA
* * * * * * *
10750 TGATTCCCAAAAATTTTAGTGAAAAAACTTTAAAGGCGTCTGTTATTGACAAACGCCTTCAGTAA
129 TGATTTCTAAAATTTTTAGTGAAAAAATTTTGAAGACGTCTGTTATTAACAAACGCCTTCAGTAA
* * * ** *
10815 TGGATTACTAAGTTTAAAGGTATATTAAAGGTACTTTTTTGAATAAACACCTTCTATAACTATCA
194 TGGATTACTAAGTTTAAAGGTATATTGAAGGTGCCTTTTTGAATAAATGCCTTCTATAACCATCA
* *
10880 TGGTAAATTGAAGGCGTTTCATAATAAAAGAAGCTTTTAATAATAAAAAAATTTTAAGAAAATTA
259 TGGTATATTGAAGGCGTTTCATAATAAAAGAACCTTTTAATAATAAAAAAATTTTAAGAAAATTA
* *
10945 TTGAAGGCATTATTATCTGCAACTGCT
324 TTAAAGGCATTATTATCTGCAAATGCT
* * * *
10972 TTCACTAATTATCTACAAACTATGATAAAAATTATTAAATGCGTCTTTCTTTGATATACGCCTTC
1 TTCACTAATTATCTACAAACTGTGATAGAAATTATTAAAT--GACTTTCTTAGATATACGCCTTC
** * *
11037 AATAACTGTGTTAAAATTTATGTGGTGGTATATAGAATGCATTTTACAGTATAAAATACCTTTAA
64 AATAACTGTGTTAAAATTTATGTGACGGTATATAGAATGCATTTTACAGTAGAAGATACCTTTAA
* *
11102 TGATTTCTAAAATTTTTAGTGAAAAAATTTTGAAGACGTCTATTATTAACAAATGCCTT-AGTAA
129 TGATTTCTAAAATTTTTAGTGAAAAAATTTTGAAGACGTCTGTTATTAACAAACGCCTTCAGTAA
** * * *
11166 TGGATTACTAAGTTTAAAGGTATATTGAATATGCCTTTTTGAATAAATGTCTTCCATAACCATCG
194 TGGATTACTAAGTTTAAAGGTATATTGAAGGTGCCTTTTTGAATAAATGCCTTCTATAACCATCA
11231 TGGTATATTGAAGGCGTTTCATAATAAAAGACACC-TTTAATAATTTAAAAAAAAATTTT-A-AA
259 TGGTATATTGAAGGCGTTTCATAATAAAAGA-ACCTTTTAATAA--T--AAAAAAATTTTAAGAA
** * *
11293 AATTATTAAAGGTGTTATTTTCTGTAAATGGCT
319 AATTATTAAAGGCATTATTATCTGCAAAT-GCT
* * *
11326 TT-ATTAATTATCTACAAACTGTGATAGAAATTATTATAGATGACTTTCTTGGATATACACCTTC
1 TTCACTAATTATCTACAAACTGTGATAGAAATTATTA-A-ATGACTTTCTTAGATATACGCCTTC
* * **
11390 AATAACTGTGTTAAAATTTGTGTGACGGTATATAGAATGCATTTTACAATAGAAGACGCCTTTAA
64 AATAACTGTGTTAAAATTTATGTGACGGTATATAGAATGCATTTTACAGTAGAAGATACCTTTAA
* * * * * *
11455 TGATTTCTCAAATTTTTAGTGAGAAAATTTTGAAGACATTTGTTAATAACAAACACCTTCAGTAA
129 TGATTTCTAAAATTTTTAGTGAAAAAATTTTGAAGACGTCTGTTATTAACAAACGCCTTCAGTAA
* * *
11520 TGGATTACTAAGTTTAAAAGTATATTGAAGGTGCCTTTTCGAATAAATGCCTTTTATAACCATCA
194 TGGATTACTAAGTTTAAAGGTATATTGAAGGTGCCTTTTTGAATAAATGCCTTCTATAACCATCA
* * * ** ** *
11585 TAGTATATTGAAGGTGTTTCATAATAAAA-TATGTCTTTAATAATCTGAAAAACTTTTGTTAAGC
259 TGGTATATTGAAGGCGTTTCATAATAAAAGAACCT-TTTAATAA--T-AAAAA-AATT-TTAAGA
* * *
11649 AAATTATTGAAA--C--TATTAATGTAGAAAATGCC
318 AAATTATT-AAAGGCATTATT-ATCT-GCAAATGCT
* *
11681 TTCACTAATTATCTACAAATTGTGATA-AGAATTATTAAAGGTG-TTGTTCTTAGATATACGCCT
1 TTCACTAATTATCTACAAACTGTGATAGA-AATTATTAAA--TGACT-TTCTTAGATATACGCCT
** * *
11744 TCAATAACCATGCTAAAATTCATGTGA
62 TCAATAACTGTGTTAAAATTTATGTGA
11771 TGATATGTTC
Statistics
Matches: 672, Mismatches: 100, Indels: 48
0.82 0.12 0.06
Matches are distributed among these distances:
350 62 0.09
351 123 0.18
352 74 0.11
353 190 0.28
354 113 0.17
355 24 0.04
356 75 0.11
357 8 0.01
358 3 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (350 bp):
TTCACTAATTATCTACAAACTGTGATAGAAATTATTAAATGACTTTCTTAGATATACGCCTTCAA
TAACTGTGTTAAAATTTATGTGACGGTATATAGAATGCATTTTACAGTAGAAGATACCTTTAATG
ATTTCTAAAATTTTTAGTGAAAAAATTTTGAAGACGTCTGTTATTAACAAACGCCTTCAGTAATG
GATTACTAAGTTTAAAGGTATATTGAAGGTGCCTTTTTGAATAAATGCCTTCTATAACCATCATG
GTATATTGAAGGCGTTTCATAATAAAAGAACCTTTTAATAATAAAAAAATTTTAAGAAAATTATT
AAAGGCATTATTATCTGCAAATGCT
Done.