Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008781.1 Corchorus capsularis cultivar CVL-1 contig08802, 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: 20339
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:831 original size:26 final size:25
Alignment explanation
Indices: 801--863 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
791 AAATTTCCAT
801 TATTTTTATAATAG-AATAATTA-AAA
1 TATTTTTATAATAGCAAT--TTAGAAA
*
826 TAATTTTTAATAATGGCAATTTAGAAA
1 T-ATTTTT-ATAATAGCAATTTAGAAA
853 TATTTTTATAA
1 TATTTTTATAA
864 AAAAATGGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 5 0.15
26 15 0.45
27 10 0.30
28 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (25 bp):
TATTTTTATAATAGCAATTTAGAAA
Found at i:1415 original size:105 final size:106
Alignment explanation
Indices: 1289--1506 Score: 384
Period size: 105 Copynumber: 2.1 Consensus size: 106
1279 ATATATATTA
*
1289 TTTTCTCCCACCCAATCAACTTTAGATAAATGTCAGCATGAGATGAGTTAAATATTAATCATACA
1 TTTTCTCCCACCCAATCAACTTTAGACAAATGTCAGCATGAGATGAGTTAAATATTAATCATACA
*
1354 ACAGTTTGGGGAT-CTTTAATAGTAAGGTATAGATATGTTT
66 ACAGTTTGAGGATACTTTAATAGTAAGGTATAGATATGTTT
1394 TTTTCTCCCACCCAATCAACTTTAGACAAATGTCAGCATGAGATGAGTTAAATATTAATCATACA
1 TTTTCTCCCACCCAATCAACTTTAGACAAATGTCAGCATGAGATGAGTTAAATATTAATCATACA
* *
1459 GCAGTTTGAGGATAACTTTAATAGTAAGTTATAGATATGTTT
66 ACAGTTTGAGGAT-ACTTTAATAGTAAGGTATAGATATGTTT
1501 TTTTCT
1 TTTTCT
1507 AACCAATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
105 75 0.70
107 32 0.30
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (106 bp):
TTTTCTCCCACCCAATCAACTTTAGACAAATGTCAGCATGAGATGAGTTAAATATTAATCATACA
ACAGTTTGAGGATACTTTAATAGTAAGGTATAGATATGTTT
Found at i:1851 original size:13 final size:13
Alignment explanation
Indices: 1833--1860 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1823 TAAACTAAAT
1833 TGCAGATTTTTAA
1 TGCAGATTTTTAA
1846 TGCAGATTTTTAA
1 TGCAGATTTTTAA
1859 TG
1 TG
1861 TAGAGTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (13 bp):
TGCAGATTTTTAA
Found at i:8726 original size:19 final size:19
Alignment explanation
Indices: 8700--8740 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
8690 CCTCTTTACT
*
8700 TTTTTTTTTC-TTTCTTTC
1 TTTTCTTTTCTTTTCTTTC
*
8718 TTTTCTTTTCTTTTCGTTC
1 TTTTCTTTTCTTTTCTTTC
8737 TTTT
1 TTTT
8741 TCTGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTCTTTTCTTTC
Found at i:10588 original size:75 final size:75
Alignment explanation
Indices: 10481--10631 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
10471 TTCAGTTGAG
10481 ATCATGATTAAATTGTTTTCTTCTTCAAAAAAAATATAGTATATCTTTTTATTTTCTTAGAAAAG
1 ATCATGATTAAATTGTTTTCTTCTTCAAAAAAAATATAGTATATCTTTTTATTTTCTTAGAAAAG
10546 AAGAAATTAA
66 AAGAAATTAA
10556 ATCATGATTAAATTGTTTTCTTCTTCAAAAAAAATATAGTATATCTTTTTATTTTCTTAGAAAAG
1 ATCATGATTAAATTGTTTTCTTCTTCAAAAAAAATATAGTATATCTTTTTATTTTCTTAGAAAAG
10621 AAGAAATTAA
66 AAGAAATTAA
10631 A
1 A
10632 AGAGGTGATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (75 bp):
ATCATGATTAAATTGTTTTCTTCTTCAAAAAAAATATAGTATATCTTTTTATTTTCTTAGAAAAG
AAGAAATTAA
Found at i:12056 original size:2 final size:2
Alignment explanation
Indices: 12044--12073 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12034 TTCATGGAGA
12044 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12074 ATTAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17676 original size:17 final size:15
Alignment explanation
Indices: 17644--17685 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
17634 CGCTCAAATG
17644 TCGGGTCATTTGGGT
1 TCGGGTCATTTGGGT
17659 TCGGGTCAATTCTGGGT
1 TCGGGTC-ATT-TGGGT
*
17676 T-GGCTCATTT
1 TCGGGTCATTT
17686 TCAGTTTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 7 0.29
17 6 0.25
ACGTcount: A:0.10, C:0.17, G:0.33, T:0.40
Consensus pattern (15 bp):
TCGGGTCATTTGGGT
Found at i:19649 original size:68 final size:69
Alignment explanation
Indices: 19533--19666 Score: 198
Period size: 68 Copynumber: 2.0 Consensus size: 69
19523 TGTCAAATCT
* *
19533 GAGCCAAAAACCTGTTAACCCCGGTTTATACATAATTTCAACTAAACACTT-AGGGGTGGTTTTA
1 GAGCCAAAAACCTGTTAACCCCAGTTTATACATAATTTCAACTAAACACTTAAAGGGTGGTTTTA
19597 ACTA
66 ACTA
* * ** *
19601 GAGCTAAAAACCTGTTAATCCCAGTTTATATGTAATTTCAACTCAACACTTAAAGGGTGGTTTTA
1 GAGCCAAAAACCTGTTAACCCCAGTTTATACATAATTTCAACTAAACACTTAAAGGGTGGTTTTA
19666 A
66 A
19667 TATCATCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 45 0.78
69 13 0.22
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (69 bp):
GAGCCAAAAACCTGTTAACCCCAGTTTATACATAATTTCAACTAAACACTTAAAGGGTGGTTTTA
ACTA
Done.