Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007549.1 Corchorus capsularis cultivar CVL-1 contig07570, 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: 35773
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:425 original size:24 final size:24
Alignment explanation
Indices: 396--448 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
386 CAGGCCTTCA
*
396 TGTCATCCTCGGGTTCGGTTTCCT
1 TGTCATCCTCGGGCTCGGTTTCCT
420 TGTCATCCTCGGGCTCGGTTTCCT
1 TGTCATCCTCGGGCTCGGTTTCCT
444 TGTCA
1 TGTCA
449 GCGGCAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.06, C:0.30, G:0.25, T:0.40
Consensus pattern (24 bp):
TGTCATCCTCGGGCTCGGTTTCCT
Found at i:6109 original size:1 final size:1
Alignment explanation
Indices: 6053--6096 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
6043 TAAATCTTCG
6053 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6097 ATAGATGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8478 original size:72 final size:72
Alignment explanation
Indices: 8315--8480 Score: 217
Period size: 72 Copynumber: 2.3 Consensus size: 72
8305 ATGTCACCTC
* * * * * *
8315 CCAATGAATTGTGAGAAAGATCTAAAGTTTGGAGATTGTAAAGTTGCCCCAAACTTTCTGGGATT
1 CCAATGAATTGTGAGAAAGATCCAAAGTTTGGAGATTGGAAAGTTGCCCAAAACATTCTGGAATG
8380 GTCCCTT
66 GTCCCTT
* * *
8387 CCAATGAATTGCGAGAAAGA-CACAAATTTTGGAGGTTGGAAAGTTGCCCAAAACATTCTGGAAT
1 CCAATGAATTGTGAGAAAGATC-CAAAGTTTGGAGATTGGAAAGTTGCCCAAAACATTCTGGAAT
8451 GGTCCCTT
65 GGTCCCTT
* *
8459 CCAATGAATTGTAATAAAGATC
1 CCAATGAATTGTGAGAAAGATC
8481 AGGGTACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.01
72 78 0.98
73 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (72 bp):
CCAATGAATTGTGAGAAAGATCCAAAGTTTGGAGATTGGAAAGTTGCCCAAAACATTCTGGAATG
GTCCCTT
Found at i:15097 original size:3 final size:3
Alignment explanation
Indices: 15089--15116 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15079 GCGGAATTAT
15089 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
15117 ACTGATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17109 original size:72 final size:73
Alignment explanation
Indices: 17020--17178 Score: 234
Period size: 72 Copynumber: 2.2 Consensus size: 73
17010 CTTCCAATGA
* *
17020 ATTGTG-GGAAAGATCTAAAGTTTCAAGGTTAGAAAGTTGCCCAAGACTTTCAGGGATGGTCCCA
1 ATTGTGAGAAAAGATCTAAAGTTTCAAGGTTAGAAAGTTGCCCAAGACTTTCAGGAATGGTCCCA
17084 TTCAATTG
66 TTCAATTG
** * * *
17092 ATTGTGAGAAAAG-TCTAAAGTTTTGAGGTTGGGAAGTTGCCCTAGACTTTCAGGAATGGTCCCA
1 ATTGTGAGAAAAGATCTAAAGTTTCAAGGTTAGAAAGTTGCCCAAGACTTTCAGGAATGGTCCCA
17156 TTCAATTG
66 TTCAATTG
17164 ATTGTGAG-AAAGATC
1 ATTGTGAGAAAAGATC
17179 AAGGTGGGTT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 4 0.05
72 69 0.88
73 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (73 bp):
ATTGTGAGAAAAGATCTAAAGTTTCAAGGTTAGAAAGTTGCCCAAGACTTTCAGGAATGGTCCCA
TTCAATTG
Found at i:29935 original size:31 final size:31
Alignment explanation
Indices: 29897--29977 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
29887 GGTGAGTGTC
*
29897 TACGGTATACCTTTGGTGGATATGGAGTATT
1 TACGGTATACCTTTGGTGGATAGGGAGTATT
*
29928 TACGGTATACCTTTGGTGGGTAGGGAGTATT
1 TACGGTATACCTTTGGTGGATAGGGAGTATT
29959 TACGGTATACCTTTTGGTG
1 TACGGTATACC-TTTGGTG
29978 AGTAATCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 40 0.85
32 7 0.15
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.38
Consensus pattern (31 bp):
TACGGTATACCTTTGGTGGATAGGGAGTATT
Found at i:30208 original size:26 final size:26
Alignment explanation
Indices: 30179--30260 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
30169 TTAATACATG
30179 ATAATATATAATTGAAATCATATATT
1 ATAATATATAATTGAAATCATATATT
* *
30205 ATAAGCATGACCAA---AAATCAT-TATCT
1 ATAA-TAT-A-TAATTGAAATCATATAT-T
*
30231 ACAATATATAATTGAAATCATATATT
1 ATAATATATAATTGAAATCATATATT
30257 ATAA
1 ATAA
30261 GCATGACCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
23 2 0.05
24 1 0.02
25 5 0.12
26 26 0.62
27 5 0.12
28 1 0.02
29 2 0.05
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (26 bp):
ATAATATATAATTGAAATCATATATT
Found at i:30238 original size:52 final size:52
Alignment explanation
Indices: 30181--30285 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
30171 AATACATGAT
*
30181 AATATATAATTGAAATCATATATTATAAGCATGACCAAAAATCATTATCTAC
1 AATATATAATTGAAATCATATATTATAAGCATGACCAAAAATCATCATCTAC
30233 AATATATAATTGAAATCATATATTATAAGCATGACCAAAAATCATCATCTAC
1 AATATATAATTGAAATCATATATTATAAGCATGACCAAAAATCATCATCTAC
30285 A
1 A
30286 GAGATCAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (52 bp):
AATATATAATTGAAATCATATATTATAAGCATGACCAAAAATCATCATCTAC
Found at i:30274 original size:26 final size:26
Alignment explanation
Indices: 30193--30277 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
30183 TATATAATTG
30193 AAATCATATATTATAAGCATGACCAA
1 AAATCATATATTATAAGCATGACCAA
* * *
30219 AAATCAT-TATCTACAA-TAT-A-TAA
1 AAATCATATAT-TATAAGCATGACCAA
30242 TTGAAATCATATATTATAAGCATGACCAA
1 ---AAATCATATATTATAAGCATGACCAA
30271 AAATCAT
1 AAATCAT
30278 CATCTACAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
23 2 0.04
24 1 0.02
25 5 0.11
26 29 0.64
27 5 0.11
28 1 0.02
29 2 0.04
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATCATATATTATAAGCATGACCAA
Found at i:35440 original size:203 final size:201
Alignment explanation
Indices: 35087--35495 Score: 631
Period size: 203 Copynumber: 2.0 Consensus size: 201
35077 GCACCTTTCG
*
35087 TTTAA-GGGTGATTATATGATACACCGGCGGTGTAAATTTTGAACTCCACAAGGGCTTGTGGAGT
1 TTTAATGGGTGATTATATGATACACCGGCAGTGTAAATTTTGAACTCCACAAGGGCTTGTGGAGT
* *
35151 TGACACATGTCCATTTTTTTAAGTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACAC
66 TGACACATGTCCATTTTTTGAAGTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACAC
* * * *
35216 ATGTCACCCTTCAGGACCCGCTTGTGTAATTTTCTAAACTCCACCGCCGGTGTATTGTATAATTT
131 ATGCCACCCTTCAGGACCCGCTTGTGTAATCTGCTAAACTCCACCGACGGTGTATTGTATAATTT
35281 GCCTTCA
196 GCCTT-A
* * * *
35288 TTTAATGGGTGATTATTTGATACACCGGCAGTGTAAATTTTGGATTCCACAAGCGGGTTGTGGAG
1 TTTAATGGGTGATTATATGATACACCGGCAGTGTAAATTTTGAACTCCACAAG-GGCTTGTGGAG
*
35353 TTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACA
65 TTGACACATGTCCATTTTTTGAAGTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACA
* * * **
35418 CATGCCACCTTTCAGGACCCGCTTGTGTAGTCTGCTAAACTTCATTGACGGTGTATTGTATAATT
130 CATGCCACCCTTCAGGACCCGCTTGTGTAATCTGCTAAACTCCACCGACGGTGTATTGTATAATT
*
35483 TGTCTTA
195 TGCCTTA
35490 TTTAAT
1 TTTAAT
35496 TTGTAATTAA
Statistics
Matches: 188, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
201 5 0.03
202 50 0.27
203 133 0.71
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (201 bp):
TTTAATGGGTGATTATATGATACACCGGCAGTGTAAATTTTGAACTCCACAAGGGCTTGTGGAGT
TGACACATGTCCATTTTTTGAAGTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACAC
ATGCCACCCTTCAGGACCCGCTTGTGTAATCTGCTAAACTCCACCGACGGTGTATTGTATAATTT
GCCTTA
Done.