Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013715.1 Corchorus olitorius cultivar O-4 contig13748, 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: 33445
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4011 original size:21 final size:22
Alignment explanation
Indices: 3974--4016 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3964 TGGTATCAAC
3974 TGTCATGAAACCCAAAAAAAAT
1 TGTCATGAAACCCAAAAAAAAT
*
3996 TGTCATGAAACCAAAAAAAAA
1 TGTCATGAAACCCAAAAAAAA
4017 AGTGGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.16
Consensus pattern (22 bp):
TGTCATGAAACCCAAAAAAAAT
Found at i:5521 original size:21 final size:22
Alignment explanation
Indices: 5474--5522 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
5464 TCGAGCCGAG
* *
5474 TAATCATTCAGGAACAAAAGAT
1 TAATCACTAAGGAACAAAAGAT
* *
5496 GAATCACTAAGGAAC-ACAGAT
1 TAATCACTAAGGAACAAAAGAT
5517 TAATCA
1 TAATCA
5523 AACTAAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (22 bp):
TAATCACTAAGGAACAAAAGAT
Found at i:9858 original size:35 final size:35
Alignment explanation
Indices: 9819--9899 Score: 92
Period size: 41 Copynumber: 2.1 Consensus size: 35
9809 CAAATACATG
9819 TACATGTCTTTTGGATAAAGACAA-TATTAAATAGA
1 TACATGTCTTTTGGATAAAGACAACT-TTAAATAGA
9854 TACATGTCTTTGTCTTTTGGATAAAGACAACTTTAAATAGA
1 TACA------TGTCTTTTGGATAAAGACAACTTTAAATAGA
9895 TACAT
1 TACAT
9900 ATATTTTCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
35 5 0.13
41 33 0.85
42 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (35 bp):
TACATGTCTTTTGGATAAAGACAACTTTAAATAGA
Found at i:9959 original size:27 final size:27
Alignment explanation
Indices: 9927--10005 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
9917 TTCTTTATTA
*
9927 ATGAATAATCACAATATTAATTAATTC
1 ATGAATAATCACATTATTAATTAATTC
*
9954 ATGAATAATCACATTATTAATTGATTC
1 ATGAATAATCACATTATTAATTAATTC
*
9981 ATGAATAATCACATTATTCATTAAT
1 ATGAATAATCACATTATTAATTAAT
10006 GTCTTTTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (27 bp):
ATGAATAATCACATTATTAATTAATTC
Found at i:11760 original size:2 final size:2
Alignment explanation
Indices: 11753--11795 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11743 ATTTATAGTG
11753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11795 T
1 T
11796 TGGGACTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15774 original size:13 final size:13
Alignment explanation
Indices: 15756--15796 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
15746 GTTGTGAGTT
15756 GAGCAATTGTGGA
1 GAGCAATTGTGGA
15769 GAGCAATCTGT-GA
1 GAGCAAT-TGTGGA
*
15782 GAGCAATCGTGGA
1 GAGCAATTGTGGA
15795 GA
1 GA
15797 AGAGCAAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 20 0.80
14 3 0.12
ACGTcount: A:0.32, C:0.12, G:0.37, T:0.20
Consensus pattern (13 bp):
GAGCAATTGTGGA
Found at i:24432 original size:178 final size:178
Alignment explanation
Indices: 24133--24453 Score: 493
Period size: 178 Copynumber: 1.8 Consensus size: 178
24123 TAAGCGCAAA
* *
24133 TTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTT
* * *
24198 TTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAACAAC
66 TTGATACCTTGAACAATAAATTTAGTTTTCAAGTCCCTCATGAAAGTTGTAGATCATGAAACAAC
24263 CTTTCAAGAGACATTTGAATCATCTCAATTAGACAACTGAAACAAAAG
131 CTTTCAAGAGACATTTGAATCATCTCAATTAGACAACTGAAACAAAAG
* * *
24311 TTATATAATATTAAGTGGACCGTTTATTCCCGTTAACTGAAACAACAAATT-TTTCGGAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GGAAGCATT
* *
24375 TTTGATA-CTTGAAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGAAACA
65 TTTGATACCTTG-AACAATAAATTTAGTTTTCAAGTCCCTCATGAAAGTTGTAGATCATGAAACA
* * *
24439 ATCTTTTAATAGACA
129 ACCTTTCAAGAGACA
24454 CTTAAATGAC
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
177 7 0.05
178 121 0.95
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGGAAGCATTT
TTGATACCTTGAACAATAAATTTAGTTTTCAAGTCCCTCATGAAAGTTGTAGATCATGAAACAAC
CTTTCAAGAGACATTTGAATCATCTCAATTAGACAACTGAAACAAAAG
Found at i:25563 original size:21 final size:21
Alignment explanation
Indices: 25537--25581 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
25527 TTTTCTTTTG
25537 CTGTTGGTCTAAATAGCAGCA
1 CTGTTGGTCTAAATAGCAGCA
25558 CTGTTGGTCTAAATAGCAGCA
1 CTGTTGGTCTAAATAGCAGCA
25579 CTG
1 CTG
25582 AACGACCAAA
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:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
CTGTTGGTCTAAATAGCAGCA
Found at i:29264 original size:13 final size:15
Alignment explanation
Indices: 29235--29279 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
29225 CTTTTTCCAC
* *
29235 TATTATTTCTCTCTA
1 TATTATTACTCTGTA
29250 TATTA-TACT-TGTA
1 TATTATTACTCTGTA
29263 TA-TATTACTCTGTA
1 TATTATTACTCTGTA
29277 TAT
1 TAT
29280 ATGGAAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.08
13 9 0.36
14 9 0.36
15 5 0.20
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (15 bp):
TATTATTACTCTGTA
Found at i:32286 original size:21 final size:21
Alignment explanation
Indices: 32260--32308 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
32250 GAAAGGAAGA
32260 CAATAACGTAAAAAAAAAAAAT
1 CAATAACG-AAAAAAAAAAAAT
* * *
32282 -AATAAAGGAAAAAGAAAAAT
1 CAATAACGAAAAAAAAAAAAT
32302 CAATAAC
1 CAATAAC
32309 CTGATTTGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.71, C:0.08, G:0.08, T:0.12
Consensus pattern (21 bp):
CAATAACGAAAAAAAAAAAAT
Found at i:32810 original size:41 final size:41
Alignment explanation
Indices: 32744--33026 Score: 363
Period size: 41 Copynumber: 6.9 Consensus size: 41
32734 GTTTGATTTG
* * *
32744 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAATTGACA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* * * * *
32784 ATCTAATTCAAAGGTCTTGACGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
32825 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 AT--TT-AATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* **
32869 ATTTAATTCATGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
32910 ATTTAATTCAAGGGTCTCGATGACTTGTTCTTAAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
32951 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
32992 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
33027 CAAATGAAAA
Statistics
Matches: 210, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
40 11 0.05
41 160 0.76
42 4 0.02
43 1 0.00
44 34 0.16
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:33143 original size:16 final size:16
Alignment explanation
Indices: 33122--33156 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
33112 TCTGAAAATA
33122 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
33138 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
33154 CTT
1 CTT
33157 TCGGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Done.