Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021070.1 Corchorus olitorius cultivar O-4 contig21103, 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: 31352
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:109 original size:67 final size:67
Alignment explanation
Indices: 1--240 Score: 383
Period size: 67 Copynumber: 3.6 Consensus size: 67
*
1 GAAGACAATCTCATTAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGAT
1 GAAGACAATCTCATTAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGAT
66 TG
66 TG
* * * **
68 GAAGACAATCTTATTAAGGAGTACACTGGAAGACAATTTGCTAGAAAGAATTTTCAAATGCTGAT
1 GAAGACAATCTCATTAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGAT
133 TG
66 TG
*
135 GAAGACAATCTCATTAAGGAATACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGCTGAT
1 GAAGACAATCTCATTAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGAT
200 TG
66 TG
* *
202 GAAGACAATCTCATTGAGGAATACA-CGAGAAGATGGTTT
1 GAAGACAATCTCATTAAGGAATACACCG-GAAGACGGTTT
241 CTCAACAATT
Statistics
Matches: 158, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
66 2 0.01
67 156 0.99
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27
Consensus pattern (67 bp):
GAAGACAATCTCATTAAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAATGCTGAT
TG
Found at i:399 original size:65 final size:64
Alignment explanation
Indices: 223--411 Score: 211
Period size: 64 Copynumber: 2.9 Consensus size: 64
213 CATTGAGGAA
* * * * * *
223 TACACGAGAAGATGGTTTCTCAACAA-TTTACAGAAGTTGATCAGAAGACGATCTTGTCAAGAAG
1 TACACCAGAAGATGTTTTCTCAAAAAGTTT-CAGAAGTTGATCGGAAGACGATCTTGTTAAAAAG
* * * *
287 TACGCCAGAAGATGTTTTGTCAAAAATTTTCAGAAGATGATCGGAAGACGATCTTGTTAAAAAG
1 TACACCAGAAGATGTTTTCTCAAAAAGTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAAG
* ** *
351 TACACCGGAATTTAG-TTTCTCGAAAAGGTTTCAGAAGTTGATCGGAAGACGATCTTGTTAA
1 TACACCAGAAGAT-GTTTTCTC-AAAAAGTTTCAGAAGTTGATCGGAAGACGATCTTGTTAA
412 GAGATGCACC
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
64 65 0.62
65 40 0.38
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (64 bp):
TACACCAGAAGATGTTTTCTCAAAAAGTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAAAAG
Found at i:683 original size:50 final size:50
Alignment explanation
Indices: 626--854 Score: 350
Period size: 50 Copynumber: 4.5 Consensus size: 50
616 TGATGTTCTC
*
626 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
**
676 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCAAAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
*
726 AAGATTGAATTAGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * * *
776 AAGATTGAATTGGAAGACAATTCAAAAGATAAGCGGGAGACAGTCCTTTTTT
1 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC--TTTT
* *
828 AAGATTGGATTGGAAGACAATTCAAAG
1 AAGATTGAATTGGAAGACAGTTCAAAG
855 AAGTTGATTC
Statistics
Matches: 164, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 135 0.82
52 29 0.18
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.24
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:869 original size:26 final size:25
Alignment explanation
Indices: 835--915 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 25
825 TTTAAGATTG
835 GATTGGAAGACAATTCAAAGAAGTT
1 GATTGGAAGACAATTCAAAGAAGTT
* ***
860 GATTCGGAAGACGATTCCCCGAAGATT
1 GATT-GGAAGACAATTCAAAGAAG-TT
887 GAATTGGAAGACAATTCAAAGAAGTT
1 G-ATTGGAAGACAATTCAAAGAAGTT
913 GAT
1 GAT
916 CAGGAGACGA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
25 6 0.13
26 18 0.40
27 18 0.40
28 3 0.07
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (25 bp):
GATTGGAAGACAATTCAAAGAAGTT
Found at i:896 original size:27 final size:26
Alignment explanation
Indices: 828--915 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 26
818 GTCCTTTTTT
828 AAGATTGGATTGGAAGACAATTCAAAG
1 AAGATT-GATTGGAAGACAATTCAAAG
* ***
855 AAG-TTGATTCGGAAGACGATTCCCCG
1 AAGATTGATT-GGAAGACAATTCAAAG
881 AAGATTGAATTGGAAGACAATTCAAAG
1 AAGATTG-ATTGGAAGACAATTCAAAG
908 AAG-TTGAT
1 AAGATTGAT
916 CAGGAGACGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 6 0.12
26 20 0.40
27 21 0.42
28 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (26 bp):
AAGATTGATTGGAAGACAATTCAAAG
Found at i:896 original size:105 final size:100
Alignment explanation
Indices: 626--906 Score: 303
Period size: 100 Copynumber: 2.8 Consensus size: 100
616 TGATGTTCTC
* * * ***
626 AAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTGAATTGGAA
1 AAGATTGAATTAGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTCCGAAGATTGAATTGGAA
* * *
691 GACAGTTCAAAGGATAAGCAAAAGACGGTCCTTTT
66 GACAATTCAAAAGATAAGCAAAAGACAGTCCTTTT
* ***
726 AAGATTGAATTAGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGAA
1 AAGATTGAATTAGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTCCGAAGATTGAATTGGAA
***
791 GACAATTCAAAAGATAAGCGGGAGACAGTCCTTTTTT
66 GACAATTCAAAAGATAAGCAAAAGACAGTCC--TTTT
* * * ** *
828 AAGATTGGATTGGAAGACAATTCAAAGAAGTTGATTCGGAAGACGATTCC-CCGAAGATTGAATT
1 AAGATTGAATTAGAAGACAATTCAAAG--GAT-AAGCGGAAGACG-GTCCTCCGAAGATTGAATT
892 GGAAGACAATTCAAA
62 GGAAGACAATTCAAA
907 GAAGTTGATC
Statistics
Matches: 157, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
100 88 0.56
102 28 0.18
104 2 0.01
105 36 0.23
106 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.24
Consensus pattern (100 bp):
AAGATTGAATTAGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTCCGAAGATTGAATTGGAA
GACAATTCAAAAGATAAGCAAAAGACAGTCCTTTT
Found at i:1607 original size:48 final size:48
Alignment explanation
Indices: 1536--1632 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
1526 TGTTAAGTGG
* *
1536 CATTTAGTCTACCCCATGTTGCATTTCATATCCCATCATTTTAGTTAT
1 CATTTAGGCTACCCCATGTTGCATTGCATATCCCATCATTTTAGTTAT
*
1584 CATTTAGGCTATCCCATGTTGCATTGCATATCCCATCATTTTAGTTAT
1 CATTTAGGCTACCCCATGTTGCATTGCATATCCCATCATTTTAGTTAT
1632 C
1 C
1633 GCTTTAGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (48 bp):
CATTTAGGCTACCCCATGTTGCATTGCATATCCCATCATTTTAGTTAT
Found at i:5153 original size:21 final size:21
Alignment explanation
Indices: 5113--5153 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5103 GTAATCAAGA
*
5113 GTTTTCAAGATTTAAATAGAG
1 GTTTTCAAGATTCAAATAGAG
5134 GTTTTCAA-ATTCAAACTAGA
1 GTTTTCAAGATTCAAA-TAGA
5154 CTTAGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
GTTTTCAAGATTCAAATAGAG
Found at i:9400 original size:27 final size:27
Alignment explanation
Indices: 9370--9438 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
9360 CTCTTATGTA
* *
9370 GCATTTTAGTCATTTGCAC-GTCTAGGG
1 GCATTTTGGTCATTTGCACATTC-AGGG
9397 GCATTTTGGTCATTTGCACATTCAGGG
1 GCATTTTGGTCATTTGCACATTCAGGG
9424 GCATTTTGGTCATTT
1 GCATTTTGGTCATTT
9439 CAAGTTCGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 37 0.95
28 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (27 bp):
GCATTTTGGTCATTTGCACATTCAGGG
Found at i:12731 original size:51 final size:51
Alignment explanation
Indices: 12671--12772 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
12661 ATTATTGATA
*
12671 TCATTGGGGTCGTTTTCAAAGTTGTGTATGATACAATAAAAAATGGGTGAG
1 TCATTGGGGTCGTTTCCAAAGTTGTGTATGATACAATAAAAAATGGGTGAG
*
12722 TCATTGGGGTCGTTTCCAAAGTTGTGTATGATACAATAAAAATTGGGTGAG
1 TCATTGGGGTCGTTTCCAAAGTTGTGTATGATACAATAAAAAATGGGTGAG
12773 ATGTCTGATC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (51 bp):
TCATTGGGGTCGTTTCCAAAGTTGTGTATGATACAATAAAAAATGGGTGAG
Found at i:15311 original size:17 final size:17
Alignment explanation
Indices: 15272--15310 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
15262 CCTCTTCTCC
* *
15272 TCTTTCATGAAAACACT
1 TCTTTTATGAAAACAAT
15289 TCTTTTATGAAAACAAT
1 TCTTTTATGAAAACAAT
15306 T-TTTT
1 TCTTTT
15311 TTAACTACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (17 bp):
TCTTTTATGAAAACAAT
Found at i:23586 original size:19 final size:18
Alignment explanation
Indices: 23553--23588 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23543 TGAAAATAAT
23553 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
23571 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
23589 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.