Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007168.1 Corchorus capsularis cultivar CVL-1 contig07189, 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: 44483
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:351 original size:12 final size:13
Alignment explanation
Indices: 336--369 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
326 AATCTAAATC
*
336 TAAAGCAGATT-A
1 TAAAGCAAATTAA
348 TAAAGCAAATTAA
1 TAAAGCAAATTAA
361 TAAAGCAAA
1 TAAAGCAAA
370 CAATAACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:2035 original size:33 final size:33
Alignment explanation
Indices: 1998--2104 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
1988 AGCACTAGTG
* *
1998 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
2031 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
2064 ACCGGCCACGCGACATGGACATGTCCGACC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
2096 AACCGGCCA
1 -ACCGGCCA
2105 TCGCTAAGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
32 2 0.03
33 60 0.97
ACGTcount: A:0.24, C:0.38, G:0.28, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:5833 original size:21 final size:21
Alignment explanation
Indices: 5807--5857 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5797 TTGAAGCCGA
5807 AAATCATGTTACCGTGTCCGC
1 AAATCATGTTACCGTGTCCGC
*
5828 AAATCATGTTACCGTGTCCGT
1 AAATCATGTTACCGTGTCCGC
5849 AAATCATGT
1 AAATCATGT
5858 AGATTGATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (21 bp):
AAATCATGTTACCGTGTCCGC
Found at i:6581 original size:2 final size:2
Alignment explanation
Indices: 6574--6603 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6564 GCGAATTTTA
*
6574 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6604 GAGTGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6980 original size:20 final size:20
Alignment explanation
Indices: 6951--6989 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6941 AAATTCAAAA
*
6951 TAAATTAAAACTACCCATTT
1 TAAATAAAAACTACCCATTT
6971 TAAATAAAAACTACCCATT
1 TAAATAAAAACTACCCATT
6990 AAAAGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAATAAAAACTACCCATTT
Found at i:8172 original size:41 final size:42
Alignment explanation
Indices: 8115--8214 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 42
8105 AGGATCAAAT
* * *
8115 GACTTGGTCTTGAATTG-ATAATTTAATTCAAGGGTCTTGGC
1 GACTTGATCTTGAATTGAATAATTTAATTCAAGGGCCTTGAC
* * *
8156 GGCTTGATCTTGAATTGATAATAATTTGATTCAAGGGCCTTGAT
1 GACTTGATCTTGAATTG--AATAATTTAATTCAAGGGCCTTGAC
8200 GACTTGATCTTGAAT
1 GACTTGATCTTGAAT
8215 AAACAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 15 0.31
44 34 0.69
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (42 bp):
GACTTGATCTTGAATTGAATAATTTAATTCAAGGGCCTTGAC
Found at i:8347 original size:44 final size:44
Alignment explanation
Indices: 8297--8380 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
8287 AATAAATTTC
8297 TTTGATAACAATCCTCCAAATAT-ATGGATCTTCTTTCAATCTTT
1 TTTGATAACAATCCTCCAAAT-TCATGGATCTTCTTTCAATCTTT
** * *
8341 TTTGATAGTAATCCTCCACATTCGTGGATCTTCTTTCAAT
1 TTTGATAACAATCCTCCAAATTCATGGATCTTCTTTCAAT
8381 AATTCTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (44 bp):
TTTGATAACAATCCTCCAAATTCATGGATCTTCTTTCAATCTTT
Found at i:11016 original size:41 final size:42
Alignment explanation
Indices: 10960--11059 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 42
10950 GGGGTCGAAT
* *
10960 GACTTGGTCTTGAATTG-ATAATTTAATTCAAGGGTCTTGGC
1 GACTTGATCTTGAATTGAATAATTTAATTCAAGGGCCTTGGC
* **
11001 GACTTGATCTTGAATTGATAATAATTTGATTCAAGGGCCTTGTT
1 GACTTGATCTTGAATTG--AATAATTTAATTCAAGGGCCTTGGC
11045 GACTTGATCTTGAAT
1 GACTTGATCTTGAAT
11060 AAACAAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
41 16 0.31
44 35 0.69
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (42 bp):
GACTTGATCTTGAATTGAATAATTTAATTCAAGGGCCTTGGC
Found at i:11182 original size:43 final size:43
Alignment explanation
Indices: 11135--11223 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
11125 TCTACAAATA
*
11135 AATTTCTTTGATAATAATCCTCCACATATGTGGATATTCTTTC
1 AATTTCTTTGATAATAATCCTCCACATACGTGGATATTCTTTC
* *
11178 AATTTTTTTGATAATAATCCTCCACATACGTGGATCTTCTTTC
1 AATTTCTTTGATAATAATCCTCCACATACGTGGATATTCTTTC
11221 AAT
1 AAT
11224 AATCCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (43 bp):
AATTTCTTTGATAATAATCCTCCACATACGTGGATATTCTTTC
Found at i:19686 original size:45 final size:45
Alignment explanation
Indices: 19621--19743 Score: 192
Period size: 45 Copynumber: 2.7 Consensus size: 45
19611 CTCCATCATT
* * *
19621 AACAAGATTAGAATCCTCTCCTTCACAAACAAATCCTTCATCAAG
1 AACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTTCATCAAG
* *
19666 AACAAAATCATAATCTTCTCCTTCACAAACATATCCTTCATCAAG
1 AACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTTCATCAAG
*
19711 AACATAATCAGAATCTTCTCCTTCACAAACAAA
1 AACAAAATCAGAATCTTCTCCTTCACAAACAAA
19744 GAGATCCTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.26
Consensus pattern (45 bp):
AACAAAATCAGAATCTTCTCCTTCACAAACAAATCCTTCATCAAG
Found at i:39672 original size:19 final size:20
Alignment explanation
Indices: 39634--39672 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39624 GCTTGGTCCC
* *
39634 TTTGCTTCCAAATTTCAATT
1 TTTGCTACCAAATCTCAATT
39654 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
39673 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTGCTACCAAATCTCAATT
Done.