Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014787.1 Corchorus olitorius cultivar O-4 contig14820, 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: 23646
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3001 original size:25 final size:25
Alignment explanation
Indices: 2943--2992 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2933 AAGAAGATTA
2943 AAACATATAGGAAGATAAAACATATG
1 AAACATA-AGGAAGATAAAACATATG
*
2969 AAATATAAGGAAGATAAAACATAT
1 AAACATAAGGAAGATAAAACATAT
2993 AGGACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (25 bp):
AAACATAAGGAAGATAAAACATATG
Found at i:3396 original size:6 final size:6
Alignment explanation
Indices: 3385--3447 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
3375 ATCCATAACT
* ** *
3385 ACGACC ACGACC ACGACC A-TAGCC AAAACC ACGACC ACGACC ACGTCC
1 ACGACC ACGACC ACGACC ACGA-CC ACGACC ACGACC ACGACC ACGACC
*
3433 ACGTCC ACGACC ACG
1 ACGACC ACGACC ACG
3448 TCCATAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.96
7 1 0.02
ACGTcount: A:0.33, C:0.46, G:0.16, T:0.05
Consensus pattern (6 bp):
ACGACC
Found at i:3434 original size:18 final size:18
Alignment explanation
Indices: 3413--3451 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3403 ATAGCCAAAA
3413 CCACGACCACGACCACGT
1 CCACGACCACGACCACGT
*
3431 CCACGTCCACGACCACGT
1 CCACGACCACGACCACGT
3449 CCA
1 CCA
3452 TAATTATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.51, G:0.15, T:0.08
Consensus pattern (18 bp):
CCACGACCACGACCACGT
Found at i:3448 original size:12 final size:12
Alignment explanation
Indices: 3413--3451 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3403 ATAGCCAAAA
*
3413 CCACGACCACGA
1 CCACGACCACGT
*
3425 CCACGTCCACGT
1 CCACGACCACGT
3437 CCACGACCACGT
1 CCACGACCACGT
3449 CCA
1 CCA
3452 TAATTATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.51, G:0.15, T:0.08
Consensus pattern (12 bp):
CCACGACCACGT
Found at i:3491 original size:28 final size:28
Alignment explanation
Indices: 3451--3506 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3441 GACCACGTCC
3451 ATAATTATAGTTTTTGTGTGTTGCTACA
1 ATAATTATAGTTTTTGTGTGTTGCTACA
3479 ATAATTATAGTTTTTGTGTGTTGCTACA
1 ATAATTATAGTTTTTGTGTGTTGCTACA
3507 TTCACTTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (28 bp):
ATAATTATAGTTTTTGTGTGTTGCTACA
Found at i:4459 original size:33 final size:33
Alignment explanation
Indices: 4419--4487 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
4409 TTTAATAATA
*
4419 AAAGAAAGGTAGAAGGAA-GAGATTATGCATGAT
1 AAAGAAAGGTAGAA-GAAGGAGATCATGCATGAT
4452 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
1 AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
4485 AAA
1 AAA
4488 TAAACTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.51, C:0.04, G:0.29, T:0.16
Consensus pattern (33 bp):
AAAGAAAGGTAGAAGAAGGAGATCATGCATGAT
Found at i:13205 original size:16 final size:16
Alignment explanation
Indices: 13184--13214 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13174 TGATAACTAA
13184 ATTACATTTATAAAAT
1 ATTACATTTATAAAAT
*
13200 ATTACATTTGTAAAA
1 ATTACATTTATAAAA
13215 AGCTATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTACATTTATAAAAT
Found at i:17617 original size:21 final size:21
Alignment explanation
Indices: 17591--17635 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
17581 TTAGATTTAG
17591 TTTTCATATCGTTGCATATGA
1 TTTTCATATCGTTGCATATGA
17612 TTTTCATATCGTTGCATATGA
1 TTTTCATATCGTTGCATATGA
17633 TTT
1 TTT
17636 GTCACGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (21 bp):
TTTTCATATCGTTGCATATGA
Found at i:19359 original size:19 final size:19
Alignment explanation
Indices: 19335--19372 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19325 AAAAAAGATT
19335 TACCCCAGTTATATTAATA
1 TACCCCAGTTATATTAATA
19354 TACCCCAGTTATATTAATA
1 TACCCCAGTTATATTAATA
19373 AGATCATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (19 bp):
TACCCCAGTTATATTAATA
Found at i:22658 original size:22 final size:22
Alignment explanation
Indices: 22629--22776 Score: 103
Period size: 22 Copynumber: 6.8 Consensus size: 22
22619 TGAATATTTT
22629 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTATCC
* * *
22651 TATTAAATTTTGATAACCA-CGT
1 TATGAAATTTTGATAACTATC-C
*
22673 TATGAAATTTTGATAA-TAACC
1 TATGAAATTTTGATAACTATCC
*
22694 TATGAAATTGTGATAA--ACTCC
1 TATGAAATTTTGATAACTA-TCC
* * *
22715 ATATTAAACTTTGATAACCTA-AC
1 -TATGAAATTTTGATAA-CTATCC
* *
22738 TATTAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTATCC
22761 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
22777 CTCTCTATGA
Statistics
Matches: 100, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.02
21 21 0.21
22 59 0.59
23 17 0.17
25 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATCC
Found at i:22746 original size:65 final size:63
Alignment explanation
Indices: 22629--22753 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 63
22619 TGAATATTTT
* * *
22629 TATGAAATTTTGATAACTATCCTATTAAATTTTGATAACCACGTTATGAAATTTTGATAATAACC
1 TATGAAATTGTGATAAC-ATCCTATTAAACTTTGATAACCACG-TATGAAATTTTAATAATAACC
*
22694 TATGAAATTGTGATAA-ACTCCATATTAAACTTTGATAACCTAAC-TATTAAATTTTAATAA
1 TATGAAATTGTGATAACA-TCC-TATTAAACTTTGATAACC--ACGTATGAAATTTTAATAA
22754 ACCTTCCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
63 1 0.02
64 3 0.06
65 46 0.88
67 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (63 bp):
TATGAAATTGTGATAACATCCTATTAAACTTTGATAACCACGTATGAAATTTTAATAATAACC
Found at i:22778 original size:44 final size:43
Alignment explanation
Indices: 22629--22776 Score: 142
Period size: 44 Copynumber: 3.4 Consensus size: 43
22619 TGAATATTTT
* * *
22629 TATGAAATTTTGATAACTATCCTATTAAATTTTGAT-AACCACGT
1 TATGAAATTTTGATAACTA-ACTATTAAATTTTGATAAACCTC-C
* *
22673 TATGAAATTTTGATAA-TAACCTATGAAATTGTGATAAA-CTCC
1 TATGAAATTTTGATAACTAA-CTATTAAATTTTGATAAACCTCC
* * *
22715 ATATTAAACTTTGATAACCTAACTATTAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAA-CTAACTATTAAATTTTGATAAACC-TCC
22761 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
22777 CTCTCTATGA
Statistics
Matches: 85, Mismatches: 12, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
43 32 0.38
44 36 0.42
45 14 0.16
46 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAACTAACTATTAAATTTTGATAAACCTCC
Found at i:22800 original size:21 final size:20
Alignment explanation
Indices: 22768--22808 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
22758 TCCTATGAAA
*
22768 TTTTGTAACCTCTCTATGAG
1 TTTTGTAACCTCACTATGAG
*
22788 TTTTGATATCCTCACTATGAG
1 TTTTG-TAACCTCACTATGAG
22809 ATCGGTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (20 bp):
TTTTGTAACCTCACTATGAG
Done.