Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006541.1 Corchorus capsularis cultivar CVL-1 contig06562, 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: 34071
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2846 original size:6 final size:6
Alignment explanation
Indices: 2830--2860 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2820 CTAAGCAAAA
2830 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
2861 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:5669 original size:21 final size:19
Alignment explanation
Indices: 5637--5675 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5627 CAATCAAGCA
5637 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
5656 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
5676 ATGGGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:8786 original size:21 final size:19
Alignment explanation
Indices: 8749--8796 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
8739 AAACCCTAAA
8749 TTTATTTTCGACAAATTTT
1 TTTATTTTCGACAAATTTT
*
8768 TTTTTTTTCGATGCAAATTTT
1 TTTATTTTCGA--CAAATTTT
8789 TTTATTTT
1 TTTATTTT
8797 AGAAAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
21 15 0.60
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTATTTTCGACAAATTTT
Found at i:9105 original size:6 final size:6
Alignment explanation
Indices: 9089--9119 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
9079 CTAAGCAAAA
9089 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
9120 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:13917 original size:31 final size:31
Alignment explanation
Indices: 13882--13977 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
13872 TTGGGTTATC
*
13882 AGTCTCCAAATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
*
13913 AGTCTCCAGATCTTTAGATCTTGAATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
13944 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
13975 AGT
1 AGT
13978 TAGTTCAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:14846 original size:3 final size:3
Alignment explanation
Indices: 14838--14867 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
14828 TTTTCACAAA
14838 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
14868 TAAGAAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17763 original size:7 final size:7
Alignment explanation
Indices: 17739--17772 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
17729 TAATGAGGTT
17739 GGTTA-G
1 GGTTATG
17745 GGTTAT-
1 GGTTATG
17751 GGTTATG
1 GGTTATG
17758 GGTTATG
1 GGTTATG
17765 GGTTATG
1 GGTTATG
17772 G
1 G
17773 AAGAATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.42
7 15 0.58
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
GGTTATG
Found at i:19703 original size:17 final size:17
Alignment explanation
Indices: 19681--19713 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19671 TTTTATGAAT
19681 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
19698 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
19714 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:23096 original size:77 final size:78
Alignment explanation
Indices: 22921--23088 Score: 275
Period size: 78 Copynumber: 2.2 Consensus size: 78
22911 TTTTTTTAAT
* * * *
22921 TAAAATAGTAAAATGGTAAGCTAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAATAAAATGGTAAACTAAAATAGTTATAAAGATATTACATTTAATTAAATAAAAATAGA
22986 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
22999 TAAAATAATAAAATGGTAAACTAAAATATTTATAAAGATATTACATTTAATTAAAT-AAAATAGA
1 TAAAATAATAAAATGGTAAACTAAAATAGTTATAAAGATATTACATTTAATTAAATAAAAATAGA
23063 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
23076 TAAAATTATAAAA
1 TAAAATAATAAAA
23089 GTTTAAACAA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 33 0.39
78 51 0.61
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (78 bp):
TAAAATAATAAAATGGTAAACTAAAATAGTTATAAAGATATTACATTTAATTAAATAAAAATAGA
GTTTTTAGTTGAG
Found at i:31445 original size:132 final size:132
Alignment explanation
Indices: 31208--31494 Score: 448
Period size: 132 Copynumber: 2.2 Consensus size: 132
31198 ACCTCTAGTC
* *
31208 CTCCATCATCATCTATATCTTATATCAATGACCAAATTGTCCACATCCCCGTGTCCCAACCACCT
1 CTCCATCCTCATCTGTATCTTATATCAATGACCAAATTGTCCACATCCCCGTGTCCCAACCACCT
* * *
31273 AGATTATCTCCCTCTGCAACATATCCCAGCATTGACCAAGGTGTCTCAGGCCCTGCTTATCCACA
66 AGATCATCTCCCACTGCAACATATCCCAGCATTGACCAAGGTGTCTCAGCCCCTGCTTATCCACA
31338 AG
131 AG
* ** * **
31340 CTCCATCCTCAGCTGTATCTTATATCAATGACCAAATTGTCCATGTCCCTGTGTCCCGGCCACCT
1 CTCCATCCTCATCTGTATCTTATATCAATGACCAAATTGTCCACATCCCCGTGTCCCAACCACCT
*
31405 AGATCATCTCCGACTGCAACATATCCCAGCATTGACCAAGGTGTCTCAGCCCCTGCTTATCCACA
66 AGATCATCTCCCACTGCAACATATCCCAGCATTGACCAAGGTGTCTCAGCCCCTGCTTATCCACA
31470 AG
131 AG
* *
31472 CTCCTTCCTCATCTGTGTCTTAT
1 CTCCATCCTCATCTGTATCTTAT
31495 CCCATCATTG
Statistics
Matches: 140, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 140 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.29
Consensus pattern (132 bp):
CTCCATCCTCATCTGTATCTTATATCAATGACCAAATTGTCCACATCCCCGTGTCCCAACCACCT
AGATCATCTCCCACTGCAACATATCCCAGCATTGACCAAGGTGTCTCAGCCCCTGCTTATCCACA
AG
Found at i:31640 original size:27 final size:27
Alignment explanation
Indices: 31610--31672 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
31600 CCTGCAATTG
* *
31610 GTGTCCAAGCACCAATTCCTGCCACAA
1 GTGTACAAGCACCAAGTCCTGCCACAA
*
31637 GTGTACAAGTACCAAGTCCTGCCACAA
1 GTGTACAAGCACCAAGTCCTGCCACAA
31664 GTGTACAAG
1 GTGTACAAG
31673 GTCAATCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (27 bp):
GTGTACAAGCACCAAGTCCTGCCACAA
Done.