Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024152.1 Corchorus olitorius cultivar O-4 contig24185, 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: 9670
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:184 original size:107 final size:104
Alignment explanation
Indices: 1--202 Score: 368
Period size: 107 Copynumber: 1.9 Consensus size: 104
*
1 ACAGCTTTGGTGCCAAAAAAAAAAAATTCTTACATACAGCTTTATGTTTCTTAGTCATGGACCCA
1 ACAGCTTTGGTGCCAAAAAAAAAAAAATCTTACATACAGCTTTATGTTTCTTAGTCATGGACCCA
66 ACACAAAAATTCAAAAACCTAAGGCCCAAAAACTTACAT
66 ACACAAAAATTCAAAAACCTAAGGCCCAAAAACTTACAT
105 ACAGCTTTGGTGCCAAAAAAAAAAAAAAATCTTAACATACAGCTTTATGTTTCTTAGTCATGGAC
1 ACAGCTTTGGTGCC--AAAAAAAAAAAAATCTT-ACATACAGCTTTATGTTTCTTAGTCATGGAC
170 CCAACACAAAAATTCAAAAACCTAAGGCCCAAA
63 CCAACACAAAAATTCAAAAACCTAAGGCCCAAA
203 TCTGAATAAC
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
104 14 0.15
106 16 0.17
107 64 0.68
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.24
Consensus pattern (104 bp):
ACAGCTTTGGTGCCAAAAAAAAAAAAATCTTACATACAGCTTTATGTTTCTTAGTCATGGACCCA
ACACAAAAATTCAAAAACCTAAGGCCCAAAAACTTACAT
Found at i:1013 original size:17 final size:17
Alignment explanation
Indices: 965--1015 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
955 CGAGTTTTGT
* *
965 AAATGGACATGCAAAGC
1 AAATTGACATGCTAAGC
982 AAATTGACCCATGCTAAGC
1 AAATTGA--CATGCTAAGC
1001 AAATTGACATGCTAA
1 AAATTGACATGCTAA
1016 ACAGTGACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.47
19 16 0.53
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATTGACATGCTAAGC
Found at i:1488 original size:11 final size:11
Alignment explanation
Indices: 1472--1498 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1462 CGTTTAAGTT
1472 TTCTTCAATTG
1 TTCTTCAATTG
1483 TTCTTCAATTG
1 TTCTTCAATTG
1494 TTCTT
1 TTCTT
1499 TCTTGTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (11 bp):
TTCTTCAATTG
Found at i:3481 original size:123 final size:129
Alignment explanation
Indices: 3245--3501 Score: 391
Period size: 123 Copynumber: 2.0 Consensus size: 129
3235 ATTTAAGAAA
3245 TATATTTAAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAATAA
1 TATATTTAAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAAT--
* *
3310 AATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAA
64 -ATA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAA
3375 AAG
127 AAG
*
3378 TATATTT-AAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-T
1 TATATTTAAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAATAT
* *
3440 A-TA-AA-GATATTATATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAATTATAAAAG
66 AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAG
3501 T
1 T
3502 TTAAACAATG
Statistics
Matches: 119, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
123 53 0.45
124 2 0.02
125 2 0.02
127 2 0.02
131 31 0.26
132 22 0.18
133 7 0.06
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.39
Consensus pattern (129 bp):
TATATTTAAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATAGTAAAAATAT
AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAG
Found at i:3633 original size:17 final size:15
Alignment explanation
Indices: 3600--3634 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
3590 CTACTTTTTA
3600 ATATAGTATAGATAG
1 ATATAGTATAGATAG
3615 ATATAGATATAGTATAG
1 ATATAG-TATAG-ATAG
3632 ATA
1 ATA
3635 AATGGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
ATATAGTATAGATAG
Found at i:6845 original size:15 final size:15
Alignment explanation
Indices: 6825--6854 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6815 TTGACGTGAA
6825 TAGATTCACTATGAG
1 TAGATTCACTATGAG
6840 TAGATTCACTATGAG
1 TAGATTCACTATGAG
6855 CTACTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TAGATTCACTATGAG
Found at i:8276 original size:2 final size:2
Alignment explanation
Indices: 8269--8303 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
8259 TTGGAAAATT
* *
8269 TA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8304 TAATTTACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9449 original size:45 final size:46
Alignment explanation
Indices: 9398--9524 Score: 222
Period size: 45 Copynumber: 2.8 Consensus size: 46
9388 AATTCTACTT
9398 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTAC-ACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTACTACTCCTC
*
9443 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATT-CTACTCTTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTACTACTCCTC
*
9488 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
9525 ATTGTTGCTT
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
44 1 0.01
45 77 0.99
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (46 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTACTACTCCTC
Done.