Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008604.1 Corchorus capsularis cultivar CVL-1 contig08625, 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: 10907
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Found at i:311 original size:25 final size:25
Alignment explanation
Indices: 283--336 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
273 TGCAAATATA
283 ATAATATCATTAATATTTTTTCTAT
1 ATAATATCATTAATATTTTTTCTAT
308 ATAATATCATTAATATTTTTTCTAT
1 ATAATATCATTAATATTTTTTCTAT
333 ATAA
1 ATAA
337 AAGAATGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAATATCATTAATATTTTTTCTAT
Found at i:1345 original size:31 final size:30
Alignment explanation
Indices: 1302--1466 Score: 110
Period size: 31 Copynumber: 5.5 Consensus size: 30
1292 ATTGGCTAAT
1302 TGCTC-AATAAGGGCCTAACATTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * * * * **
1332 TGTTCAAATAAGGGTTCGATCTTT--TAATT
1 TGCTCAAATAAGGG-CCTAACTTTGCCAAAA
1361 TGAC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAAC-TTTGCCAAAA
* * **
1392 TGCTCAAATAAGGGCCCCATCTTTG--AATT
1 TGCTCAAATAAGGG-CCTAACTTTGCCAAAA
1421 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGCCAAAA
*
1452 TACTCAAATAAGGGC
1 TGCTCAAATAAGGGC
1467 ATGTCTCATG
Statistics
Matches: 99, Mismatches: 23, Indels: 25
0.67 0.16 0.17
Matches are distributed among these distances:
28 7 0.07
29 34 0.34
30 8 0.08
31 43 0.43
32 7 0.07
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGCCAAAA
Found at i:1374 original size:60 final size:60
Alignment explanation
Indices: 1307--1466 Score: 248
Period size: 60 Copynumber: 2.7 Consensus size: 60
1297 CTAATTGCTC
* * ** * *
1307 AATAAGGGCCTAACATTTGCCAAAATGTTCAAATAAGGGTTCGATCTTTTAATTTGACCA
1 AATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGACCA
*
1367 AATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGCCA
1 AATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGACCA
*
1427 AATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGGC
1 AATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1467 ATGTCTCATG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (60 bp):
AATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGACCA
Found at i:1445 original size:29 final size:30
Alignment explanation
Indices: 1357--1446 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
1347 TCGATCTTTT
*
1357 AATTTGACCAAATAAGGGCCTAACGTTTGCC
1 AATTTGGCCAAATAAGGGCCTAACGTTTG-C
** * *
1388 AAAAT-GCTCAAATAAGGGCCCCATC-TTTG-
1 AATTTGGC-CAAATAAGGG-CCTAACGTTTGC
1417 AATTTGGCCAAATAAGGGCCTAACGTTTGC
1 AATTTGGCCAAATAAGGGCCTAACGTTTGC
1447 CAAAATACTC
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
28 4 0.09
29 17 0.38
30 3 0.07
31 17 0.38
32 4 0.09
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (30 bp):
AATTTGGCCAAATAAGGGCCTAACGTTTGC
Found at i:1534 original size:31 final size:29
Alignment explanation
Indices: 1496--1663 Score: 101
Period size: 31 Copynumber: 5.6 Consensus size: 29
1486 AACTGACACC
1496 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT
** * *
1527 AGGCCCTTATTTG-GCCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGAAACG-TT
* *
1556 GGGCCCTTATTTGAGCATTTTCGATAACATT
1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT
* ** * *
1587 AGGCTCTTATTTG-GCCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGAAACG-TT
* *
1616 ATGCCCTTATTTAAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-G-AAACGTT
1647 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
1664 ATTAGCCAAA
Statistics
Matches: 99, Mismatches: 26, Indels: 24
0.66 0.17 0.16
Matches are distributed among these distances:
28 5 0.05
29 34 0.34
30 4 0.04
31 50 0.51
32 6 0.06
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTGAAACGTT
Found at i:1590 original size:60 final size:60
Alignment explanation
Indices: 1495--1659 Score: 260
Period size: 60 Copynumber: 2.8 Consensus size: 60
1485 AAACTGACAC
1495 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * *
1555 CGGGCCCTTATTTGAGCATTTTCGATAACATTAGGCTCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * *
1615 CATGCCCTTATTTAAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
1660 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:3850 original size:15 final size:16
Alignment explanation
Indices: 3820--3850 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3810 AAAAAGTCCT
3820 AAACCAAAATTGACCC
1 AAACCAAAATTGACCC
3836 AAACCAAAA-TGACCC
1 AAACCAAAATTGACCC
3851 GACATTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.32, G:0.06, T:0.10
Consensus pattern (16 bp):
AAACCAAAATTGACCC
Found at i:6825 original size:16 final size:16
Alignment explanation
Indices: 6797--6864 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
6787 TAAATTAATT
6797 TATAGTA-CTAATATTA
1 TATAGTATC-AATATTA
6813 TATAGTATCAATATATA
1 TATAGTATCAATAT-TA
* ** * *
6830 TTTTTTTGTTAATATTA
1 -TATAGTATCAATATTA
6847 TATAGTATCAATA-TA
1 TATAGTATCAATATTA
6862 TAT
1 TAT
6865 TTGTTAATTC
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
15 5 0.13
16 20 0.51
17 5 0.13
18 9 0.23
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (16 bp):
TATAGTATCAATATTA
Found at i:6869 original size:30 final size:31
Alignment explanation
Indices: 6805--6872 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 31
6795 TTTATAGTAC
6805 TAATATTATATAGTATCAATATATATTTTTTTGT
1 TAATATTATATAGTATCAATATATA---TTTTGT
6839 TAATATTATATAGTATCAATATATA-TTTGT
1 TAATATTATATAGTATCAATATATATTTTGT
6869 TAAT
1 TAAT
6873 TCAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 9 0.26
34 25 0.74
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (31 bp):
TAATATTATATAGTATCAATATATATTTTGT
Found at i:7250 original size:27 final size:27
Alignment explanation
Indices: 7208--7267 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
7198 ACATCCTGCA
* *
7208 AAATACTTGCTTTGTTTTCCACAGACT
1 AAATATTTGCTATGTTTTCCACAGACT
*
7235 AAATATTTGCTATGTTTTCCACCGACT
1 AAATATTTGCTATGTTTTCCACAGACT
7262 AAATAT
1 AAATAT
7268 CAGTGACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (27 bp):
AAATATTTGCTATGTTTTCCACAGACT
Found at i:9664 original size:21 final size:21
Alignment explanation
Indices: 9640--9683 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
9630 CTCTAGTCAC
9640 AGGATCATACCTGTCGGTAAG
1 AGGATCATACCTGTCGGTAAG
9661 AGGATCATACCTGTCGGTAAG
1 AGGATCATACCTGTCGGTAAG
9682 AG
1 AG
9684 AATTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (21 bp):
AGGATCATACCTGTCGGTAAG
Done.