Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024815.1 Corchorus olitorius cultivar O-4 contig24848, 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: 15094
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Found at i:497 original size:22 final size:19
Alignment explanation
Indices: 469--518 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 19
459 GGTTAAGAAC
469 AAGAAAAACAAATAAACTGGAA
1 AAGAAAAA-AAATAAA--GGAA
491 AAGAAAAGAAAATAAAGGAA
1 AAGAAAA-AAAATAAAGGAA
*
511 AAGGAAAA
1 AAGAAAAA
519 GGAACTGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.38
22 14 0.54
23 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (19 bp):
AAGAAAAAAAATAAAGGAA
Found at i:2271 original size:24 final size:25
Alignment explanation
Indices: 2242--2292 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
2232 ATAGAGTAAC
*
2242 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
2266 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
2291 AA
1 AA
2293 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:2770 original size:27 final size:28
Alignment explanation
Indices: 2720--2772 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2710 AAATCAATTA
*
2720 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACACAAAGATAAATCT
2748 GAAATCATAAAATAC-CAAA-ATAAAT
1 GAAATCATAAAA-ACACAAAGATAAAT
2773 AATCATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (28 bp):
GAAATCATAAAAACACAAAGATAAATCT
Found at i:3658 original size:19 final size:19
Alignment explanation
Indices: 3634--3673 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3624 CTTACCATTC
3634 GAAAACAATTTCCTAAACT
1 GAAAACAATTTCCTAAACT
3653 GAAAACAATTTCCTAAACT
1 GAAAACAATTTCCTAAACT
3672 GA
1 GA
3674 GAGATTGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (19 bp):
GAAAACAATTTCCTAAACT
Found at i:4294 original size:14 final size:14
Alignment explanation
Indices: 4275--4305 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4265 ATATCTTTAA
4275 CATTTAAGCATTTG
1 CATTTAAGCATTTG
4289 CATTTAAGCATTTG
1 CATTTAAGCATTTG
4303 CAT
1 CAT
4306 AGGCTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (14 bp):
CATTTAAGCATTTG
Found at i:4377 original size:20 final size:20
Alignment explanation
Indices: 4339--4378 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4329 GGAAATACAA
*
4339 GGCATTTGATTTACTAATTG
1 GGCATTTGATTTACAAATTG
*
4359 GGCATTTGATTTGCAAATTG
1 GGCATTTGATTTACAAATTG
4379 ATGCTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (20 bp):
GGCATTTGATTTACAAATTG
Found at i:10471 original size:21 final size:21
Alignment explanation
Indices: 10445--10504 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
10435 TATACAATAT
10445 AAACCCTAAGTGAGATAAAAG
1 AAACCCTAAGTGAGATAAAAG
* * **
10466 AAACCCTAA--AAAATAAATT
1 AAACCCTAAGTGAGATAAAAG
*
10485 AAACCCTAGGTGAGATAAAA
1 AAACCCTAAGTGAGATAAAA
10505 ATAAAAAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (21 bp):
AAACCCTAAGTGAGATAAAAG
Found at i:10977 original size:16 final size:16
Alignment explanation
Indices: 10956--10994 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10946 ATATTTGTTG
*
10956 ATATATAATATATATA
1 ATATATAATACATATA
*
10972 ATATATATTACATATA
1 ATATATAATACATATA
*
10988 ATTTATA
1 ATATATA
10995 CGTACTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATATAATACATATA
Found at i:13507 original size:12 final size:13
Alignment explanation
Indices: 13484--13520 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
13474 CATCGATGTC
13484 ATATACTCATATCT
1 ATATACT-ATATCT
13498 ATAT-CTATATCT
1 ATATACTATATCT
13510 ATATACTATAT
1 ATATACTATAT
13521 AAGTCTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.45
13 8 0.36
14 4 0.18
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATACTATATCT
Found at i:13801 original size:21 final size:21
Alignment explanation
Indices: 13777--13843 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
13767 GTAATATAAA
13777 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
13798 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
13818 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
13840 TAAT
1 TAAT
13844 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Done.