Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009760.1 Corchorus capsularis cultivar CVL-1 contig09781, 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: 8425
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Found at i:1439 original size:22 final size:22
Alignment explanation
Indices: 1408--1530 Score: 97
Period size: 22 Copynumber: 5.6 Consensus size: 22
1398 CTACAACGTA
* *
1408 GAAATATTGATAACCTTATTAT
1 GAAATTTTGATAACCTTACTAT
* *
1430 GAAATTTTGATAA-ATTCCCTAT
1 GAAATTTTGATAACCTT-ACTAT
*
1452 G-AATATTTGATAACCATACTAT
1 GAAAT-TTTGATAACCTTACTAT
* **
1474 AAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCTTACTAT
* * * * *
1496 AAAATTTCGATAACCTCAGTGT
1 GAAATTTTGATAACCTTACTAT
1518 GAAATTTTGATAA
1 GAAATTTTGATAA
1531 TCTCCCATCA
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
21 5 0.06
22 73 0.89
23 4 0.05
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (22 bp):
GAAATTTTGATAACCTTACTAT
Found at i:1630 original size:22 final size:22
Alignment explanation
Indices: 1457--1637 Score: 124
Period size: 22 Copynumber: 8.5 Consensus size: 22
1447 CCTATGAATA
*
1457 TTTGATAACCATACTATAAAAT
1 TTTGATAACCACACTATAAAAT
1479 TTTGATAACCACACTATAAAAT
1 TTTGATAACCACACTATAAAAT
* * * * *
1501 TTCGATAACCTCAGTGTGAAAT
1 TTTGATAACCACACTATAAAAT
* * * *
1523 TTTGATAATCTC-CCATCAAAT
1 TTTGATAACCACACTATAAAAT
*
1544 TTAT-ATAATCACACTATAAAA-
1 TT-TGATAACCACACTATAAAAT
* * * **
1565 -TTGGTGACCGCACTACGCAAAT
1 TTTGATAACCACACTA-TAAAAT
*
1587 TTTGATAA-C-CTC-ATAAAAT
1 TTTGATAACCACACTATAAAAT
* *
1606 TTTGATAACCACACCATGAAAT
1 TTTGATAACCACACTATAAAAT
1628 TTTGATAACC
1 TTTGATAACC
1638 TTCCTATAAG
Statistics
Matches: 122, Mismatches: 28, Indels: 18
0.73 0.17 0.11
Matches are distributed among these distances:
19 13 0.11
20 11 0.09
21 21 0.17
22 72 0.59
23 5 0.04
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (22 bp):
TTTGATAACCACACTATAAAAT
Found at i:1705 original size:22 final size:22
Alignment explanation
Indices: 1677--1733 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1667 AATGAATAAT
* * *
1677 GAAATTTTGGTAGCCATTGTAA
1 GAAATTTTGATAACCACTGTAA
1699 GAAATTTTGATAACCACTGTAA
1 GAAATTTTGATAACCACTGTAA
1721 GAAATTTTGATAA
1 GAAATTTTGATAA
1734 ATACACTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAACCACTGTAA
Found at i:1769 original size:44 final size:44
Alignment explanation
Indices: 1699--1818 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 44
1689 GCCATTGTAA
* * * *
1699 GAAATTTTGATAACCACTGTAAGAAATTTTGATAA-ATACACTAT
1 GAAATTTTGATAACCTC-CTATGAAATTTTGACAACATACACTAT
* * **
1743 GAAGTTTTGATAACCTCCATATGAAATTTTGGCAACATGTACTAT
1 GAAATTTTGATAACCTCC-TATGAAATTTTGACAACATACACTAT
* *
1788 GAAATTTCGATAACCTTCCTATGTAATTTTG
1 GAAATTTTGATAACC-TCCTATGAAATTTTG
1819 GTTTGATTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
44 28 0.45
45 31 0.50
46 3 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (44 bp):
GAAATTTTGATAACCTCCTATGAAATTTTGACAACATACACTAT
Found at i:3807 original size:12 final size:12
Alignment explanation
Indices: 3790--3815 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3780 CTCAAATCCA
3790 TGTGACCTATGT
1 TGTGACCTATGT
3802 TGTGACCTATGT
1 TGTGACCTATGT
3814 TG
1 TG
3816 GATTGGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (12 bp):
TGTGACCTATGT
Found at i:5886 original size:41 final size:41
Alignment explanation
Indices: 5841--5922 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
5831 ACTTCAAACA
* * *
5841 TTGCTTCAAAATATACGAAATTTAACAATCATTATCCCATT
1 TTGCTTCAAAACATACGAAAGTTAACAACCATTATCCCATT
5882 TTGCTTCAAAACATACGAAAGTTAACAACCATTATCCCATT
1 TTGCTTCAAAACATACGAAAGTTAACAACCATTATCCCATT
5923 AATTGCTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (41 bp):
TTGCTTCAAAACATACGAAAGTTAACAACCATTATCCCATT
Found at i:6636 original size:381 final size:381
Alignment explanation
Indices: 5933--6696 Score: 1528
Period size: 381 Copynumber: 2.0 Consensus size: 381
5923 AATTGCTGCT
5933 TAACGGATGTACCCGTTATCTATCCTTGATTAATTTGAATTTGAGTCACTTAAAATCTAAATGCT
1 TAACGGATGTACCCGTTATCTATCCTTGATTAATTTGAATTTGAGTCACTTAAAATCTAAATGCT
5998 AAGAAGGGTCTTGACTAATGTACATATCAATTCGTGTAGAACCCTAAATGGGGTACACTGAGTCC
66 AAGAAGGGTCTTGACTAATGTACATATCAATTCGTGTAGAACCCTAAATGGGGTACACTGAGTCC
6063 TAATTAATTCTAAGTTAGGCTGTGTTGAATCTCAAACAAGAAGGAATTCTCTTACTAAATAATAT
131 TAATTAATTCTAAGTTAGGCTGTGTTGAATCTCAAACAAGAAGGAATTCTCTTACTAAATAATAT
6128 AATTTAAAGGGCATTAAGCTTTTTTCACCTAGATTGCGAACAACAGATTAATATAATTTAAGTAA
196 AATTTAAAGGGCATTAAGCTTTTTTCACCTAGATTGCGAACAACAGATTAATATAATTTAAGTAA
6193 TATACAAGCCTTGCTTAAGGATATAATAATCATATATAATATTAAAATATAATCATATAGTTCTC
261 TATACAAGCCTTGCTTAAGGATATAATAATCATATATAATATTAAAATATAATCATATAGTTCTC
6258 ATTAAAATAAGACTGCGAACAACAGATTAATTATATGATTACAAAATCCATATATA
326 ATTAAAATAAGACTGCGAACAACAGATTAATTATATGATTACAAAATCCATATATA
6314 TAACGGATGTACCCGTTATCTATCCTTGATTAATTTGAATTTGAGTCACTTAAAATCTAAATGCT
1 TAACGGATGTACCCGTTATCTATCCTTGATTAATTTGAATTTGAGTCACTTAAAATCTAAATGCT
6379 AAGAAGGGTCTTGACTAATGTACATATCAATTCGTGTAGAACCCTAAATGGGGTACACTGAGTCC
66 AAGAAGGGTCTTGACTAATGTACATATCAATTCGTGTAGAACCCTAAATGGGGTACACTGAGTCC
6444 TAATTAATTCTAAGTTAGGCTGTGTTGAATCTCAAACAAGAAGGAATTCTCTTACTAAATAATAT
131 TAATTAATTCTAAGTTAGGCTGTGTTGAATCTCAAACAAGAAGGAATTCTCTTACTAAATAATAT
6509 AATTTAAAGGGCATTAAGCTTTTTTCACCTAGATTGCGAACAACAGATTAATATAATTTAAGTAA
196 AATTTAAAGGGCATTAAGCTTTTTTCACCTAGATTGCGAACAACAGATTAATATAATTTAAGTAA
6574 TATACAAGCCTTGCTTAAGGATATAATAATCATATATAATATTAAAATATAATCATATAGTTCTC
261 TATACAAGCCTTGCTTAAGGATATAATAATCATATATAATATTAAAATATAATCATATAGTTCTC
6639 ATTAAAATAAGACTGCGAACAACAGATTAATTATATGATTACAAAATCCATATATA
326 ATTAAAATAAGACTGCGAACAACAGATTAATTATATGATTACAAAATCCATATATA
6695 TA
1 TA
6697 TATATACATA
Statistics
Matches: 383, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
381 383 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (381 bp):
TAACGGATGTACCCGTTATCTATCCTTGATTAATTTGAATTTGAGTCACTTAAAATCTAAATGCT
AAGAAGGGTCTTGACTAATGTACATATCAATTCGTGTAGAACCCTAAATGGGGTACACTGAGTCC
TAATTAATTCTAAGTTAGGCTGTGTTGAATCTCAAACAAGAAGGAATTCTCTTACTAAATAATAT
AATTTAAAGGGCATTAAGCTTTTTTCACCTAGATTGCGAACAACAGATTAATATAATTTAAGTAA
TATACAAGCCTTGCTTAAGGATATAATAATCATATATAATATTAAAATATAATCATATAGTTCTC
ATTAAAATAAGACTGCGAACAACAGATTAATTATATGATTACAAAATCCATATATA
Done.