Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009275.1 Corchorus capsularis cultivar CVL-1 contig09296, 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: 26952
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Found at i:1007 original size:19 final size:18
Alignment explanation
Indices: 983--1018 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
973 TGAAGATTTC
983 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
1002 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
1019 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:3225 original size:44 final size:44
Alignment explanation
Indices: 3153--3246 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
3143 TTGGATTTTC
*
3153 AAACATTTGTTTTCCAAAAGTCTTCTTTTGG-GTTTGCTAAAAAA
1 AAACATTTATTTTCCAAAAGTCTTCTTTTGGAG-TTGCTAAAAAA
* *
3197 AAACCTTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCT-TAAAA
1 AAACATTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCTAAAAAA
3240 AAACATT
1 AAACATT
3247 CTTTTTGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 10 0.22
44 34 0.76
45 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (44 bp):
AAACATTTATTTTCCAAAAGTCTTCTTTTGGAGTTGCTAAAAAA
Found at i:7224 original size:29 final size:29
Alignment explanation
Indices: 7164--7224 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
7154 AATGCTAATT
* **
7164 AAATTACTAAATGAAGTTAAAACAATTTC
1 AAATTACTAAATGAAGATAAAACAATGCC
**
7193 AAATTACTAAATGAAGATGCAACAATGCC
1 AAATTACTAAATGAAGATAAAACAATGCC
7222 AAA
1 AAA
7225 AGTACACATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (29 bp):
AAATTACTAAATGAAGATAAAACAATGCC
Found at i:12521 original size:42 final size:42
Alignment explanation
Indices: 12475--12558 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
12465 CATGGGACAA
*
12475 CGCACGGGACATCGCACGAGCCATCTGGCCACAACCGGCCAT
1 CGCACGGGACATCGCACGAGCCATCCGGCCACAACCGGCCAT
* * *
12517 CGCACGGGCCATCGCATGGGCCATCCGGCCACAACCGGCCAT
1 CGCACGGGACATCGCACGAGCCATCCGGCCACAACCGGCCAT
12559 TCGACCCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.42, G:0.27, T:0.10
Consensus pattern (42 bp):
CGCACGGGACATCGCACGAGCCATCCGGCCACAACCGGCCAT
Found at i:12528 original size:12 final size:12
Alignment explanation
Indices: 12511--12541 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12501 GGCCACAACC
12511 GGCCATCGCACG
1 GGCCATCGCACG
*
12523 GGCCATCGCATG
1 GGCCATCGCACG
12535 GGCCATC
1 GGCCATC
12542 CGGCCACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.39, G:0.32, T:0.13
Consensus pattern (12 bp):
GGCCATCGCACG
Found at i:14580 original size:33 final size:33
Alignment explanation
Indices: 14543--14649 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
14533 AGCACTAGTG
* *
14543 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* *
14576 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* * *
14609 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
14641 AACCGGCCA
1 -ACCGGCCA
14650 TCGCTAGGCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 2 0.03
33 62 0.97
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
Found at i:17113 original size:33 final size:32
Alignment explanation
Indices: 17076--17196 Score: 145
Period size: 33 Copynumber: 3.7 Consensus size: 32
17066 AAAGGATCAT
17076 GTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTGGCCGGGCATGGCC-ATGTCAA
**
17109 GTGGCCGGGTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATGGCCATGTCAA
**
17142 GTGGCCGGTGATGGCCGGGCATGGCCATGTCGC
1 GTGGCCGGTG-TGGCCGGGCATGGCCATGTCAA
*
17175 GTGGCCGGTGTTGCGCGGGCAT
1 GTGGCCGGTGTGGC-CGGGCAT
17197 CTCCAAGTCG
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.10
33 71 0.88
34 2 0.02
ACGTcount: A:0.08, C:0.26, G:0.47, T:0.19
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATGGCCATGTCAA
Found at i:17157 original size:66 final size:66
Alignment explanation
Indices: 17076--17218 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
17066 AAAGGATCAT
* *
17076 GTGGCCGGTTG-TGGCCGGGCATGGCCGA-GTCAAGTGGCCGGGTGTGGC-CGGGCATGGCCATG
1 GTGGCCGG-TGATGGCCGGGCATGGCC-ATGTCAAGTGGCC-GGTGTGGCGCGGGCATCGCCAAG
17138 TCGC
63 TCGC
** * *
17142 GTGGCCGGTGATGGCCGGGCATGGCCATGTCGCGTGGCCGGTGTTGCGCGGGCATCTCCAAGTCG
1 GTGGCCGGTGATGGCCGGGCATGGCCATGTCAAGTGGCCGGTGTGGCGCGGGCATCGCCAAGTCG
17207 C
66 C
*
17208 GTGGCCTGTGA
1 GTGGCCGGTGA
17219 CTTATCATGG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
65 10 0.15
66 57 0.85
ACGTcount: A:0.09, C:0.27, G:0.45, T:0.20
Consensus pattern (66 bp):
GTGGCCGGTGATGGCCGGGCATGGCCATGTCAAGTGGCCGGTGTGGCGCGGGCATCGCCAAGTCG
C
Found at i:17207 original size:33 final size:33
Alignment explanation
Indices: 17076--17213 Score: 140
Period size: 33 Copynumber: 4.2 Consensus size: 33
17066 AAAGGATCAT
* **
17076 GTGGCCGGTTGTGGC-CGGGCATGGCCGA-GTCAA
1 GTGGCCGG-TGTTGCGCGGGCATGGCC-ATGTCGC
*
17109 GTGGCCGGGTGTGGC-CGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTTGCGCGGGCATGGCCATGTCGC
*
17142 GTGGCCGGTGATG-GCCGGGCATGGCCATGTCGC
1 GTGGCCGGTGTTGCG-CGGGCATGGCCATGTCGC
** *
17175 GTGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTTGCGCGGGCATGGCCATGTCGC
17208 GTGGCC
1 GTGGCC
17214 TGTGACTTAT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
32 6 0.07
33 83 0.90
34 3 0.03
ACGTcount: A:0.09, C:0.28, G:0.45, T:0.19
Consensus pattern (33 bp):
GTGGCCGGTGTTGCGCGGGCATGGCCATGTCGC
Found at i:21372 original size:8 final size:8
Alignment explanation
Indices: 21359--21392 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
21349 CACCTTCTTG
21359 AAAAATTC
1 AAAAATTC
21367 AAAAATTC
1 AAAAATTC
*
21375 AGAAACTTC
1 A-AAAATTC
21384 AAAAATTC
1 AAAAATTC
21392 A
1 A
21393 TAACCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:26868 original size:21 final size:21
Alignment explanation
Indices: 26842--26883 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
26832 AGCACAAGTG
*
26842 ACCGGCCATGCGACTTGGAGA
1 ACCGGCCACGCGACTTGGAGA
26863 ACCGGCCACGCGACTTGGAGA
1 ACCGGCCACGCGACTTGGAGA
26884 TGCCCGCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.33, T:0.12
Consensus pattern (21 bp):
ACCGGCCACGCGACTTGGAGA
Found at i:26909 original size:33 final size:33
Alignment explanation
Indices: 26863--26946 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
26853 GACTTGGAGA
*
26863 ACCGGCCACGCGACTTGGAGATGCCCGCG-CAAC
1 ACCGGCCACGCGACATGGAGATGCCCG-GTCAAC
* * *
26896 ACCGGCCATGCGACATGGAGATGCCTGGTCATC
1 ACCGGCCACGCGACATGGAGATGCCCGGTCAAC
26929 ACCGGCCACGCGACATGG
1 ACCGGCCACGCGACATGG
26947 CCATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 44 0.98
ACGTcount: A:0.21, C:0.36, G:0.31, T:0.12
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCGGTCAAC
Done.