Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006198.1 Corchorus capsularis cultivar CVL-1 contig06216, 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: 43637
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7991 original size:156 final size:153
Alignment explanation
Indices: 7447--7986 Score: 574
Period size: 157 Copynumber: 3.5 Consensus size: 153
7437 ATCTCAAACA
*
7447 GACTTA-AGATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTTGGGGTGAGAAACC-ACT
1 GACTTAGA-ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACT
* ** * *
7510 TCACTATGATAGGGAGTTTGTTTTACTTAGAATTTTTTCCATAGTCTTATGGAAATAGTCTAAGT
65 TCACCATGATAGGGAGTCGGTTTTACTTAGAATTTTTTCCATAGTATTATGGAAATAATCTAAGT
* * * *
7575 CTCGTGGCCAAGTTTCATCTCAATTG
130 CCCTTGG-CAAATTTCAGCTC-ATTG
* * **
7601 GACTTAGTATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGGGGTGTCAAACCAACTT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTT
* * *
7666 CTCTAT-ACTAGGGAGTCCGGTTTTTACTTAGAATTTTTTCCATAGTATTATGGAGATAATCTAA
66 CACCATGA-TAGGGAGT-CGG-TTTTACTTAGAATTTTTTCCATAGTATTATGGAAATAATCTAA
* *
7730 G-CCTACTGGTGG-AAA-ATCAGCCTTATTG
128 GTCC--CT--TGGCAAATTTCAG-CTCATTG
* * *
7758 GACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGGGGAGAGAAACCAAGTT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTT
* * * *
7823 CACCATCA-AGGAGAGCTCGGTTTTACTTGGAATTTTTTCCATAGTATTGTGGAAAGAATCTAAG
66 CACCATGATAGG-GAG-TCGGTTTTACTTAGAATTTTTTCCATAGTATTATGGAAATAATCTAAG
*
7887 TCCCTTGGCAAATTTTCAGCTCATTCA
129 TCCCTTGGCAAA-TTTCAGCTCATT-G
* * * * * * *
7914 GATTTAGAATGAAAAACTTATGCTAGTTATTCA-TGTAAGGACAGTTTGAGGTGTGAAGCCTAGT
1 GACTTAGAATGAAAAACTTATGCTAGTTTTTCAGT-TAAGGACAGTTTGGGGTGAGAAACCAACT
7978 TCACCATGA
65 TCACCATGA
7987 AGGAGGGCTC
Statistics
Matches: 326, Mismatches: 41, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
153 3 0.01
154 58 0.18
155 25 0.08
156 112 0.34
157 118 0.36
158 7 0.02
160 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (153 bp):
GACTTAGAATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTT
CACCATGATAGGGAGTCGGTTTTACTTAGAATTTTTTCCATAGTATTATGGAAATAATCTAAGTC
CCTTGGCAAATTTCAGCTCATTG
Found at i:8595 original size:6 final size:6
Alignment explanation
Indices: 8586--8612 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8576 AAAGCAAAGC
8586 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
8613 GCAGATTAAT
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:8627 original size:13 final size:13
Alignment explanation
Indices: 8609--8643 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
8599 AATCTAAATC
*
8609 TAAAGCAGATTAA
1 TAAAGCAAATTAA
8622 TAAAGCAAATTAA
1 TAAAGCAAATTAA
8635 TAAAGCAAA
1 TAAAGCAAA
8644 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:16591 original size:35 final size:35
Alignment explanation
Indices: 16545--16613 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
16535 AAATCGCAAC
* **
16545 TTTTTTTTTAGAAAAATCGGAAAAAGGAAAAACTT
1 TTTTTTTTTAGAAAAAACGGAAAAAACAAAAACTT
16580 TTTTTTTTTAGAAAAAACGGAAAAAACAAAAACT
1 TTTTTTTTTAGAAAAAACGGAAAAAACAAAAACT
16614 AATTCTTGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (35 bp):
TTTTTTTTTAGAAAAAACGGAAAAAACAAAAACTT
Found at i:18388 original size:11 final size:11
Alignment explanation
Indices: 18374--18414 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
18364 AGTAAAAAGT
18374 CTCCAAAATAG
1 CTCCAAAATAG
18385 CTCCAAAA-AGG
1 CTCCAAAATA-G
18396 CTCCAAAATAG
1 CTCCAAAATAG
18407 CTCCAAAA
1 CTCCAAAA
18415 AGAGTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 26 0.93
12 1 0.04
ACGTcount: A:0.46, C:0.29, G:0.10, T:0.15
Consensus pattern (11 bp):
CTCCAAAATAG
Found at i:18399 original size:22 final size:22
Alignment explanation
Indices: 18367--18416 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
18357 ATAGTTGAGT
*
18367 AAAAAGTCTCCAAAATAGCTCC
1 AAAAAGGCTCCAAAATAGCTCC
18389 AAAAAGGCTCCAAAATAGCTCC
1 AAAAAGGCTCCAAAATAGCTCC
18411 AAAAAG
1 AAAAAG
18417 AGTGAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAAAGGCTCCAAAATAGCTCC
Found at i:26517 original size:14 final size:13
Alignment explanation
Indices: 26494--26522 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26484 GGCAATTCCG
26494 TTAGAAAAAAAAA
1 TTAGAAAAAAAAA
26507 TTAGAAAAAAAAA
1 TTAGAAAAAAAAA
26520 TTA
1 TTA
26523 AATAGCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (13 bp):
TTAGAAAAAAAAA
Found at i:26771 original size:17 final size:17
Alignment explanation
Indices: 26749--26781 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26739 AAGATTACCA
26749 GTGATCTTGCATCACTG
1 GTGATCTTGCATCACTG
*
26766 GTGATCTTGGATCACT
1 GTGATCTTGCATCACT
26782 AGTAATCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (17 bp):
GTGATCTTGCATCACTG
Found at i:27582 original size:33 final size:33
Alignment explanation
Indices: 27512--27582 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
27502 CTTAGGAGGG
* *
27512 CGGCATGCCATGGACATAGCCGCCCTCCGGGGG
1 CGGCATGCCATAGACATAGCCGCCCTCCGGGGA
* * * *
27545 CGGCATGCCATAGACATTGTCTCCCTCCTGGGA
1 CGGCATGCCATAGACATAGCCGCCCTCCGGGGA
27578 CGGCA
1 CGGCA
27583 CCGACAACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.17
Consensus pattern (33 bp):
CGGCATGCCATAGACATAGCCGCCCTCCGGGGA
Found at i:40975 original size:29 final size:28
Alignment explanation
Indices: 40926--40981 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
40916 CATTATTAGA
*
40926 AATTTCTAATGTGGCCTTTTTTATATTGG
1 AATTTCTAATGTGG-CTTTTTAATATTGG
40955 AATTTCTAATGTCGG-TGTTTTAATATT
1 AATTTCTAATGT-GGCT-TTTTAATATT
40982 TTTTGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 21 0.88
30 2 0.08
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (28 bp):
AATTTCTAATGTGGCTTTTTAATATTGG
Done.