Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006755.1 Corchorus capsularis cultivar CVL-1 contig06776, 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: 11842
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1541 original size:13 final size:13
Alignment explanation
Indices: 1523--1549 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1513 ATAATTATTG
1523 TTTGCTTTATTAA
1 TTTGCTTTATTAA
1536 TTTGCTTTATTAA
1 TTTGCTTTATTAA
1549 T
1 T
1550 CTGTTTTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:1565 original size:6 final size:6
Alignment explanation
Indices: 1554--1580 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1544 ATTAATCTGT
1554 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1581 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:6476 original size:40 final size:40
Alignment explanation
Indices: 6415--6740 Score: 332
Period size: 40 Copynumber: 7.8 Consensus size: 40
6405 GTCTTATTCT
6415 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
* * * *
6455 AATTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGCTTATTCCT
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA------AATTCCC
6501 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATT-CC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
*
6540 AGTTTGCCCTTCCTCATCGGATGGTGTTGTTTAAA-TCACC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTC-CC
* *
6580 AGTTTGCCCTTTCTCATCGGAAGGTGTTGTTTAGTTGCTTATTCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA------AATTCCC
* ** **
6626 AGTTTGCCTTTCCTCAAAGGAAGGTGTTGTTTACTTTTCCC
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-AATTCCC
* * * * *
6667 AGTTCGTCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCA
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
* * *
6707 AGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTAA
1 AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA
6741 TTTTGTCTTA
Statistics
Matches: 241, Mismatches: 30, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.00
39 35 0.15
40 102 0.42
41 33 0.14
46 68 0.28
47 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.38
Consensus pattern (40 bp):
AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC
Found at i:6508 original size:86 final size:85
Alignment explanation
Indices: 6371--6788 Score: 410
Period size: 86 Copynumber: 4.9 Consensus size: 85
6361 TTATTCCCGT
* * *
6371 TTTGCCCTTCCCCACCGGAACGTGTTGTCTAATTGTCTTATT-CTAGTTTGCCCTTCCTCATCGG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTG-CTTATTCCTAGTTTGCCCTTCCTCATCGG
6435 AAGGTGTTGTTTAAATTCCCAA
65 AAGGTGTTGTTTAAATT-CCAA
*
6457 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTGCTTATTCCTAGTTTGCCCTTCCTCATCGGA
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTGCTTATTCCTAGTTTGCCCTTCCTCATCGGA
*
6522 AGGTGTTGTTTAAATTCCAG
66 AGGTGTTGTTTAAATTCCAA
* * * *
6542 TTTGCCCTTCCTCATCGGATGGTGTTGTTTAAAT-C--A--CC-AGTTTGCCCTTTCTCATCGGA
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTGCTTATTCCTAGTTTGCCCTTCCTCATCGGA
* *
6601 AGGTGTTGTTTAGTTGCTTATTCCCAG
66 AGGTGTTGTTTA------AATT-CCAA
* ** * * * * *
6628 TTTGCCTTTCCTCAAAGGAAGGTGTTGTTT-A---CTT-TTCCCAGTTCGTCCTTCCCCACCGGA
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTGCTTATTCCTAGTTTGCCCTTCCTCATCGGA
6688 AGGTGTTGTTTAAATTCCAA
66 AGGTGTTGTTTAAATTCCAA
* * * **
6708 GTTTGCCCTTCCCCACCGGAAAGTGTTGTTTAATTTTGTCTTATTCCTATTTTGCCCTTCCTGGT
1 -TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAA--TTG-CTTATTCCTAGTTTGCCCTTCCTCAT
*
6773 CGGAAGTTGTTGTTTA
62 CGGAAGGTGTTGTTTA
6789 GTTTTATCTT
Statistics
Matches: 274, Mismatches: 36, Indels: 41
0.78 0.10 0.12
Matches are distributed among these distances:
79 32 0.12
80 5 0.02
81 28 0.10
82 2 0.01
83 1 0.00
84 1 0.00
85 43 0.16
86 102 0.37
87 28 0.10
88 3 0.01
89 29 0.11
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (85 bp):
TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAATTGCTTATTCCTAGTTTGCCCTTCCTCATCGGA
AGGTGTTGTTTAAATTCCAA
Found at i:6589 original size:125 final size:127
Alignment explanation
Indices: 6315--6788 Score: 528
Period size: 125 Copynumber: 3.7 Consensus size: 127
6305 CGGTTCACTT
*
6315 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCC-CGTTTTGCCCT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTAG-TTTGCCCT
* * * * *
6379 TCCCCACCGGAACGTGTTGTCTAATTGTCTTATTCTAGTTTGCCCTTCCTCATCGGAAGGTGTTG
65 TCCTCATCGGAAGGTGTTGTTTAA-------ATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG
6444 TTTAA
123 TTTAA
* *
6449 ATTCCCAATTTGCCCTTCCTCACCGGAAGGTGTTGTTT-AGTTG-CTTATTCCTAGTTTGCCCTT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTAGTTTGCCCTT
*
6512 CCTCATCGGAAGGTGTTGTTTAAATTCCAGTTTGCCCTTCCTCATCGGATGGTGTTGTTTAA
66 CCTCATCGGAAGGTGTTGTTTAAATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA
* * * * *
6574 A-TCACCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTTT-AGTTG-CTTATTCCCAGTTTGCCTT
1 ATTC-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTAGTTTGCCCT
** ** * * * *
6636 TCCTCAAAGGAAGGTGTTGTTTACTTTTCCCAGTTCGTCCTTCCCCACCGGAAGGTGTTGTTTAA
65 TCCTCATCGGAAGGTGTTGTTTA-AATT-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA
* * * * *
6701 ATTCCAAGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTAATTTTGTCTTATTCCTATTTTGCCCT
1 ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA-GTTGCCTTATTCCTAGTTTGCCCT
** *
6766 TCCTGGTCGGAAGTTGTTGTTTA
65 TCCTCATCGGAAGGTGTTGTTTA
6789 GTTTTATCTT
Statistics
Matches: 295, Mismatches: 37, Indels: 20
0.84 0.11 0.06
Matches are distributed among these distances:
124 2 0.01
125 112 0.38
126 2 0.01
127 61 0.21
128 3 0.01
129 3 0.01
130 34 0.12
132 36 0.12
133 6 0.02
134 36 0.12
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.40
Consensus pattern (127 bp):
ATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAGTTGCCTTATTCCTAGTTTGCCCTT
CCTCATCGGAAGGTGTTGTTTAAATTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA
Found at i:6762 original size:49 final size:50
Alignment explanation
Indices: 6709--6825 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 50
6699 AAATTCCAAG
*
6709 TTTGCCCTTCCCCACCGGAAAG-TGTTGTTTAATTTTGTCTTATTCCTAT
1 TTTGCCCTTCCCCACCGGAAAGTTGTTGTTTAATTTTATCTTATTCCTAT
**** * * *
6758 TTTGCCCTTCCTGGTCGG-AAGTTGTTGTTTAGTTTTATCTTATTCTTGT
1 TTTGCCCTTCCCCACCGGAAAGTTGTTGTTTAATTTTATCTTATTCCTAT
*
6807 TTTGCTCTT-CCCACCGGAA
1 TTTGCCCTTCCCCACCGGAA
6826 GGTATTGCTC
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
48 7 0.13
49 46 0.87
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (50 bp):
TTTGCCCTTCCCCACCGGAAAGTTGTTGTTTAATTTTATCTTATTCCTAT
Done.