Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024084.1 Corchorus olitorius cultivar O-4 contig24117, 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: 20922
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:1780 original size:42 final size:42
Alignment explanation
Indices: 1719--1830 Score: 188
Period size: 42 Copynumber: 2.6 Consensus size: 42
1709 TAACGTACTT
* *
1719 TATATACTACCGAGTGGAGGAGCTCAATTCGAATATGTATATG
1 TATATACTATCAAG-GGAGGAGCTCAATTCGAATATGTATATG
1762 TATATACTATCAAGGGAGGAGCTCAATTCGAATATGTATATG
1 TATATACTATCAAGGGAGGAGCTCAATTCGAATATGTATATG
*
1804 TATATACTATCAAGGGAGGAGTTCAAT
1 TATATACTATCAAGGGAGGAGCTCAAT
1831 ATGAATTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
42 54 0.82
43 12 0.18
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (42 bp):
TATATACTATCAAGGGAGGAGCTCAATTCGAATATGTATATG
Found at i:2040 original size:21 final size:20
Alignment explanation
Indices: 2006--2045 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1996 TAATAAAATC
*
2006 TCATAGGAAGGTTATCAAAAA
1 TCATAAGAAGGTTA-CAAAAA
*
2027 TCATAAGAATGTTACAAAA
1 TCATAAGAAGGTTACAAAA
2046 TTTCATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
TCATAAGAAGGTTACAAAAA
Found at i:2051 original size:21 final size:22
Alignment explanation
Indices: 2000--2185 Score: 60
Period size: 22 Copynumber: 8.5 Consensus size: 22
1990 GGAGATTAAT
* *
2000 AAAATCTCATAGGAAGGTTATC
1 AAAATATCATAAGAAGGTTATC
*
2022 AAAA-ATCATAAGAATGTTA-C
1 AAAATATCATAAGAAGGTTATC
* * * *
2042 AAAATTTCATATGAGGGTTTATT
1 AAAATATCATAAGAAGG-TTATC
* ***
2065 AAAATTTCATATTTAGGTTATC
1 AAAATATCATAAGAAGGTTATC
* * * * *
2087 AAAGTTTCATATGGAGTTTATC
1 AAAATATCATAAGAAGGTTATC
* * *
2109 ACAATTTCATAGGTAA--TTATC
1 AAAATATCATAAG-AAGGTTATC
* * *
2130 AAAATTTCATAGGGTA-GTTATC
1 AAAATATCATA-AGAAGGTTATC
* * *
2152 AAAATTTAATAAGGTA-GTTATC
1 AAAATATCATAA-GAAGGTTATC
*
2174 AAAATTTCATAA
1 AAAATATCATAA
2186 AAATATTTAA
Statistics
Matches: 132, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.04
21 36 0.27
22 76 0.58
23 15 0.11
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (22 bp):
AAAATATCATAAGAAGGTTATC
Found at i:2106 original size:44 final size:43
Alignment explanation
Indices: 2037--2184 Score: 165
Period size: 44 Copynumber: 3.4 Consensus size: 43
2027 TCATAAGAAT
* * **
2037 GTTA-CAAAATTTCATATGAGGGTTTATTAAAATTTCATATTTA
1 GTTATCAAAATTTCATATG-GAGTTTATCAAAATTTCATAGGTA
* *
2080 GGTTATCAAAGTTTCATATGGAGTTTATCACAATTTCATAGGTA
1 -GTTATCAAAATTTCATATGGAGTTTATCAAAATTTCATAGGTA
* * *
2124 ATTATCAAAATTTCATAGGGTAG-TTATCAAAATTTAATAAGGTA
1 GTTATCAAAATTTCATATGG-AGTTTATCAAAATTTCAT-AGGTA
2168 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
2185 AAAATATTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
43 30 0.34
44 46 0.52
45 13 0.15
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (43 bp):
GTTATCAAAATTTCATATGGAGTTTATCAAAATTTCATAGGTA
Found at i:2107 original size:22 final size:22
Alignment explanation
Indices: 2037--2184 Score: 144
Period size: 22 Copynumber: 6.8 Consensus size: 22
2027 TCATAAGAAT
*
2037 GTTA-CAAAATTTCATATGAG-G
1 GTTATCAAAATTTCATATG-GTA
* *
2058 GTTTATTAAAATTTCATAT-TTA
1 G-TTATCAAAATTTCATATGGTA
*
2080 GGTTATCAAAGTTTCATATGG-A
1 -GTTATCAAAATTTCATATGGTA
*
2102 GTTTATCACAATTTCATA-GGTA
1 G-TTATCAAAATTTCATATGGTA
* *
2124 ATTATCAAAATTTCATAGGGTA
1 GTTATCAAAATTTCATATGGTA
* *
2146 GTTATCAAAATTTAATAAGGTA
1 GTTATCAAAATTTCATATGGTA
2168 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
2185 AAAATATTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 15
0.78 0.10 0.11
Matches are distributed among these distances:
21 19 0.18
22 73 0.70
23 13 0.12
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGGTA
Found at i:4164 original size:17 final size:17
Alignment explanation
Indices: 4142--4177 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4132 ATATATTATA
4142 TTAATGTTCCCATCAAC
1 TTAATGTTCCCATCAAC
4159 TTAATGTTCCCATCAAC
1 TTAATGTTCCCATCAAC
4176 TT
1 TT
4178 TCTGTAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (17 bp):
TTAATGTTCCCATCAAC
Found at i:9737 original size:42 final size:43
Alignment explanation
Indices: 9678--9770 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
9668 TGCTAGGAGA
9678 TCATTGGAGCAAGTTCCAAGCTCA-TTGGAGAAGGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGCTCATTTGGAGAAGGTTCCAAGC
*
9720 TCATTGGAG-AAGTTTCCAAGCTCATTTGGAGAAGTTTCCAAGC
1 TCATTGGAGCAAG-TTCCAAGCTCATTTGGAGAAGGTTCCAAGC
9763 TCATTGGA
1 TCATTGGA
9771 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 3 0.06
42 20 0.42
43 25 0.52
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TCATTGGAGCAAGTTCCAAGCTCATTTGGAGAAGGTTCCAAGC
Found at i:9751 original size:22 final size:21
Alignment explanation
Indices: 9678--9770 Score: 152
Period size: 21 Copynumber: 4.4 Consensus size: 21
9668 TGCTAGGAGA
9678 TCATTGGAGCAAG-TTCCAAGC
1 TCATTGGAG-AAGTTTCCAAGC
*
9699 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGTTTCCAAGC
9720 TCATTGGAGAAGTTTCCAAGC
1 TCATTGGAGAAGTTTCCAAGC
9741 TCATTTGGAGAAGTTTCCAAGC
1 TCA-TTGGAGAAGTTTCCAAGC
9763 TCATTGGA
1 TCATTGGA
9771 ATTGCCTAAG
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
20 3 0.04
21 45 0.65
22 21 0.30
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGTTTCCAAGC
Found at i:10687 original size:26 final size:23
Alignment explanation
Indices: 10645--10691 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
10635 TCCTTCTATT
10645 CATCTATCATCAAGTTTTTCATC
1 CATCTATCATCAAGTTTTTCATC
10668 CATCTCATCCATCTAAGTTTTTCA
1 CATCT-AT-CATC-AAGTTTTTCA
10692 AATTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.26, C:0.28, G:0.04, T:0.43
Consensus pattern (23 bp):
CATCTATCATCAAGTTTTTCATC
Found at i:15472 original size:21 final size:20
Alignment explanation
Indices: 15443--15513 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 20
15433 TGCTAGGAGA
15443 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAG-AAGTTCCAAGC
* *
15464 TCTTTGGAGAAGGTTTCAAGC
1 TCATTGGAGAA-GTTCCAAGC
15485 TCATTGGAGAAGTTTCCAAGC
1 TCATTGGAGAAG-TTCCAAGC
15506 TCATTGGA
1 TCATTGGA
15514 ATTGCCTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.07
21 41 0.93
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
TCATTGGAGAAGTTCCAAGC
Done.