Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022020.1 Corchorus olitorius cultivar O-4 contig22053, 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: 26791
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3550 original size:46 final size:46
Alignment explanation
Indices: 3461--3631 Score: 256
Period size: 46 Copynumber: 3.7 Consensus size: 46
3451 TTGAAGCAAA
* * * *
3461 AGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAAGCCGATGCAG
1 AGGTAGAGGGCAAT-AAATAATCAACCCCGCCAATAAGTCGATGCAG
3508 AGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGTCGATGCAG
1 AGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGTCGATGCAG
*
3554 AGGTAGAGGGCGATAAATAATCAACCCCGCC-A-AAGTCGATGCAG
1 AGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGTCGATGCAG
* *
3598 AGGTAGAGGGTAATAAATAATCAACGCCGCCAAT
1 AGGTAGAGGGCAATAAATAATCAACCCCGCCAAT
3632 GTTGAAAGGA
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
44 40 0.35
45 2 0.02
46 59 0.52
47 13 0.11
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (46 bp):
AGGTAGAGGGCAATAAATAATCAACCCCGCCAATAAGTCGATGCAG
Found at i:3617 original size:90 final size:93
Alignment explanation
Indices: 3461--3631 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 93
3451 TTGAAGCAAA
3461 AGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCAATAAAT
1 AGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCAATAAAT
3526 AATCAACCCCGCCAATAAGTCGATGCAG
66 AATCAACCCCGCCAATAAGTCGATGCAG
* * *
3554 AGGTAGAGGGCGAT-AAATAATCAACCCCGCC-A-AAGTCGATGCAGAGGTAGAGGGTAATAAAT
1 AGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCAATAAAT
*
3616 AATCAACGCCGCCAAT
66 AATCAACCCCGCCAAT
3632 GTTGAAAGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
90 43 0.58
91 1 0.01
92 16 0.22
93 14 0.19
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (93 bp):
AGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAAGCCGATGCAGAGGTAGAGGGCAATAAAT
AATCAACCCCGCCAATAAGTCGATGCAG
Found at i:5684 original size:16 final size:16
Alignment explanation
Indices: 5663--5693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5653 CTGTCTTCCA
*
5663 TTCTTCTTCTTCTTCG
1 TTCTTCTTATTCTTCG
5679 TTCTTCTTATTCTTC
1 TTCTTCTTATTCTTC
5694 CAACAACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.65
Consensus pattern (16 bp):
TTCTTCTTATTCTTCG
Found at i:8635 original size:76 final size:76
Alignment explanation
Indices: 8510--8705 Score: 315
Period size: 76 Copynumber: 2.6 Consensus size: 76
8500 TAAGATCACT
* * *
8510 TTCCAGATTTCCCTTGATAAGTTAC-TGGCTTATCCTTTTGTTTGGTCTACAAACTCTTCAATGT
1 TTCCATATTTTCCTTGATAAGTTACTTGCCTTATCCTTTTGTTTGGTCTACAAACTCTTCAATGT
8574 ATGTAATTACC
66 ATGTAATTACC
* *
8585 TTCCATATTTTCCTTGATAAGTTACTTGCCTTATCCTTTTGTTTTGTCTACAAACTCTTTAATGT
1 TTCCATATTTTCCTTGATAAGTTACTTGCCTTATCCTTTTGTTTGGTCTACAAACTCTTCAATGT
8650 ATGTAATTACC
66 ATGTAATTACC
*
8661 TTCCATA-TTTCCGATGATAAGTTACTTGCCTTATCCTTTTGTTTG
1 TTCCATATTTTCC-TTGATAAGTTACTTGCCTTATCCTTTTGTTTG
8706 ATGTGAAAAT
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
75 28 0.25
76 84 0.75
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (76 bp):
TTCCATATTTTCCTTGATAAGTTACTTGCCTTATCCTTTTGTTTGGTCTACAAACTCTTCAATGT
ATGTAATTACC
Found at i:9455 original size:44 final size:44
Alignment explanation
Indices: 9405--9496 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
9395 TAAGCAATCC
9405 AAGCCAAAGTAAGTTGAGAATTTGTGCTTGGCTACAAAATTTTG
1 AAGCCAAAGTAAGTTGAGAATTTGTGCTTGGCTACAAAATTTTG
9449 AAGCCAAAGTAAGTTGAGAATTTGTGCTTGGCTACAAAATTTTG
1 AAGCCAAAGTAAGTTGAGAATTTGTGCTTGGCTACAAAATTTTG
9493 AAGC
1 AAGC
9497 TTGGATCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (44 bp):
AAGCCAAAGTAAGTTGAGAATTTGTGCTTGGCTACAAAATTTTG
Found at i:10134 original size:35 final size:34
Alignment explanation
Indices: 10085--10203 Score: 94
Period size: 46 Copynumber: 3.1 Consensus size: 34
10075 AGCAAATCTG
*
10085 AAGCTAAGTTTTCTCCATCAACAAAGCAACAACA
1 AAGCAAAGTTTTCTCCATCAACAAAGCAACAACA
10119 AAGCAAAGTTCTTCTCCATTTCTTCTCCATCAACAAAGCAACAACA
1 AAGCAAAG------T---TTTC---TCCATCAACAAAGCAACAACA
* *
10165 AAGCAAAGTTGTTTTCCATCAACAAAGCAACAAAA
1 AAGCAAAGTT-TTCTCCATCAACAAAGCAACAACA
10200 AAGC
1 AAGC
10204 CTACGAAAGT
Statistics
Matches: 69, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
34 7 0.10
35 24 0.35
37 1 0.01
38 2 0.03
40 2 0.03
43 4 0.06
46 29 0.42
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (34 bp):
AAGCAAAGTTTTCTCCATCAACAAAGCAACAACA
Found at i:10146 original size:46 final size:46
Alignment explanation
Indices: 10095--10183 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
10085 AAGCTAAGTT
10095 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTC
1 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTC
* *
10141 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTGTTTTCCAT
1 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCAT
10184 CAACAAAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (46 bp):
TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATTTC
Found at i:10433 original size:40 final size:42
Alignment explanation
Indices: 10350--10440 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 42
10340 TCAAATCTAG
*
10350 CAAATCCGACAACGAGGAATAACAAGCCTTCAGCCATTTCTCT
1 CAAATCC-ACAACGAGGAATAACAAGCCTTCAGCCATTCCTCT
** *
10393 CAAATCCACAACGA-GAA-AACAAGCCTTTGGTCATTCCTCT
1 CAAATCCACAACGAGGAATAACAAGCCTTCAGCCATTCCTCT
*
10433 CATATCCA
1 CAAATCCA
10441 TTTCATCGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 26 0.60
41 3 0.07
42 7 0.16
43 7 0.16
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (42 bp):
CAAATCCACAACGAGGAATAACAAGCCTTCAGCCATTCCTCT
Found at i:10685 original size:32 final size:32
Alignment explanation
Indices: 10641--10701 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
10631 CCGCTTATCT
*
10641 TTTGGTTGTTCATGACTTTGCACTATGCATTG
1 TTTGGTTGTTCATGAATTTGCACTATGCATTG
*
10673 TTTGGTTTTTCATGAATTTGCACTATGCA
1 TTTGGTTGTTCATGAATTTGCACTATGCA
10702 CTGCTCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.48
Consensus pattern (32 bp):
TTTGGTTGTTCATGAATTTGCACTATGCATTG
Found at i:20361 original size:57 final size:58
Alignment explanation
Indices: 20294--20436 Score: 198
Period size: 57 Copynumber: 2.4 Consensus size: 58
20284 CCCCCAAAAC
* *
20294 TAAAAGGTGAAAGTTCCAAATTAAAAATTCAGGAGGATAA-ACCCAATTTTGATAATT
1 TAAAAGGTGAAAGTTCCAAATTAAAAATTCACGAGGATAATACACAATTTTGATAATT
* *
20351 TAAAAGGTGAAAGTTCCAAATTAAAAATTCACGAGGATAATTGTCACAATTTTGATAGTT
1 TAAAAGGTGAAAGTTCCAAATTAAAAATTCACGAGGATAA-T-ACACAATTTTGATAATT
** *
20411 TAAGGGGTGAAAGTTTCAAATTAAAA
1 TAAAAGGTGAAAGTTCCAAATTAAAA
20437 TTTTAAGGGG
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
57 39 0.51
60 37 0.49
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (58 bp):
TAAAAGGTGAAAGTTCCAAATTAAAAATTCACGAGGATAATACACAATTTTGATAATT
Found at i:22904 original size:29 final size:29
Alignment explanation
Indices: 22820--22906 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
22810 TTAATGCTCT
* **
22820 TTTTGTCCCCTAAACTTGTTCAATTTTAACG
1 TTTTGGCCCCTAAACTTG--CAATTTGGACG
*
22851 TTTTGGCCCCTAAACTT-TAATTTTGGACG
1 TTTTGGCCCCTAAACTTGCAA-TTTGGACG
22880 TTTT-GCACCCTAAACTTGCAATTTGGA
1 TTTTGGC-CCCTAAACTTGCAATTTGGA
22907 ACCATTTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.08
29 26 0.54
30 2 0.04
31 16 0.33
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTTGGCCCCTAAACTTGCAATTTGGACG
Found at i:22983 original size:13 final size:13
Alignment explanation
Indices: 22965--23016 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
22955 TCGAATCAAA
22965 AATGCCACGTGGC
1 AATGCCACGTGGC
22978 AATGCCACGTCGGATC
1 AATGCCACGT-GG--C
22994 AAAATGCCACGTGGC
1 --AATGCCACGTGGC
*
23009 AAGGCCAC
1 AATGCCAC
23017 ATCGGACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 17 0.52
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 10 0.30
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (13 bp):
AATGCCACGTGGC
Found at i:23001 original size:31 final size:32
Alignment explanation
Indices: 22945--23022 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
22935 GCTGATGTGA
*
22945 CAATGCCACGTCGAATCAAAAATGCCACGTGG
1 CAATGCCACGTCGGATCAAAAATGCCACGTGG
22977 CAATGCCACGTCGGATC-AAAATGCCACGTGG
1 CAATGCCACGTCGGATCAAAAATGCCACGTGG
* *
23008 CAAGGCCACATCGGA
1 CAATGCCACGTCGGA
23023 CCAAGACGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
31 27 0.63
32 16 0.37
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.14
Consensus pattern (32 bp):
CAATGCCACGTCGGATCAAAAATGCCACGTGG
Found at i:23125 original size:29 final size:28
Alignment explanation
Indices: 23093--23147 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
23083 TCCAAATTGC
*
23093 AAGTTTAGGGGCCAAAACGTCCAAAATTA
1 AAGTTTAGGGGCCAAAACAT-CAAAATTA
*
23122 AAGTTTAGGGGGCAAAACATCAAAAT
1 AAGTTTAGGGGCCAAAACATCAAAAT
23148 CGTGTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (28 bp):
AAGTTTAGGGGCCAAAACATCAAAATTA
Done.