Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015789.1 Corchorus olitorius cultivar O-4 contig15822, 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: 66821
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11746 original size:21 final size:21
Alignment explanation
Indices: 11720--11759 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11710 ATGAGATTAA
*
11720 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTATGT
11741 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
11760 TAGAGCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:14348 original size:24 final size:24
Alignment explanation
Indices: 14321--14369 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
14311 CATTCTTGTC
14321 CCTACCTTAGCTAGAAATGTCAAA
1 CCTACCTTAGCTAGAAATGTCAAA
14345 CCTACCTTAGCTAGAAATGTCAAA
1 CCTACCTTAGCTAGAAATGTCAAA
14369 C
1 C
14370 AATGGCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (24 bp):
CCTACCTTAGCTAGAAATGTCAAA
Found at i:31641 original size:31 final size:33
Alignment explanation
Indices: 31603--31676 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
31593 TTAGATGTGT
31603 TGACGAGTTAAT-AC-TTT-TTTTTTTGGCACAA
1 TGACGAGTTAATAACTTTTCTTTTTTTGGCA-AA
31634 TGACGAG-TAATACACTTTTCTTTTTTTGGCAAA
1 TGACGAGTTAATA-ACTTTTCTTTTTTTGGCAAA
*
31667 GGACGAGTTA
1 TGACGAGTTA
31677 TTAGTTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 4 0.11
31 7 0.19
32 2 0.05
33 11 0.30
34 13 0.35
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (33 bp):
TGACGAGTTAATAACTTTTCTTTTTTTGGCAAA
Found at i:32911 original size:22 final size:22
Alignment explanation
Indices: 32881--32937 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
32871 ACCCCCCATC
*
32881 AAATTTTGATAACTACCCTTT-
1 AAATGTTGATAACTACCCTTTG
*
32902 ATAATGTTGATAACTGCCCTTTG
1 A-AATGTTGATAACTACCCTTTG
*
32925 AAATTTTGATAAC
1 AAATGTTGATAAC
32938 CATTTATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (22 bp):
AAATGTTGATAACTACCCTTTG
Found at i:33068 original size:66 final size:67
Alignment explanation
Indices: 32908--33069 Score: 181
Period size: 66 Copynumber: 2.4 Consensus size: 67
32898 CTTTATAATG
* * * * *
32908 TTGATAACTGCCCTTTGAAATTTTGATAACCATTTATATTTTAATTTTGATAACCTTGATTGAAA
1 TTGACAACTACCCTATGAAATTTTGATAAACATTTATATTTTAATTTTAATAACCTTGATTGAAA
32973 TT
66 TT
*
32975 TTGACAACTACCCTAT-ATAATTATGATAAACATTT-T-TTTGTAATTTTAATAA-CTTCGATTG
1 TTGACAACTACCCTATGA-AATTTTGATAAACATTTATATTT-TAATTTTAATAACCTT-GATTG
33036 AAATT
63 AAATT
**
33041 TTGACAA-TCATTCTATGAAATTTTGATAA
1 TTGACAACT-ACCCTATGAAATTTTGATAA
33070 CTACTGTTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
65 7 0.09
66 45 0.56
67 29 0.36
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (67 bp):
TTGACAACTACCCTATGAAATTTTGATAAACATTTATATTTTAATTTTAATAACCTTGATTGAAA
TT
Found at i:33081 original size:22 final size:22
Alignment explanation
Indices: 33056--33239 Score: 115
Period size: 22 Copynumber: 8.5 Consensus size: 22
33046 AATCATTCTA
* **
33056 TGAAATTTTGATAACTACTGTT
1 TGAAATTTTGATAACCACCATT
* *
33078 TGAAATTTCGAAAACCACCATT
1 TGAAATTTTGATAACCACCATT
*
33100 TGAAATTTTGATAACCACAATT
1 TGAAATTTTGATAACCACCATT
** * ***
33122 TTTAATTTTCATAACCTTGA-T
1 TGAAATTTTGATAACCACCATT
* * *
33143 TGAAGTTTTGATAACGACCCTT
1 TGAAATTTTGATAACCACCATT
* * *
33165 T-ATAAATTTGATAACC-TCATA
1 TGA-AATTTTGATAACCACCATT
* * *
33186 TGAAATTTTGGTAACCATCTTT
1 TGAAATTTTGATAACCACCATT
* *
33208 TAAAATTTTGATAACCTCCA-T
1 TGAAATTTTGATAACCACCATT
*
33229 TAAAATTTTGA
1 TGAAATTTTGA
33240 AAAATACCTC
Statistics
Matches: 120, Mismatches: 38, Indels: 9
0.72 0.23 0.05
Matches are distributed among these distances:
21 39 0.32
22 81 0.68
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCACCATT
Found at i:33179 original size:43 final size:43
Alignment explanation
Indices: 33099--33239 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
33089 AAACCACCAT
* * * * *
33099 TTGAAATTTTGATAACCACAATTTTTAATTTTCATAACCTTGA
1 TTGAAATTTTGATAACCACCATTTATAAATTTGATAACCTTCA
* * *
33142 TTGAAGTTTTGATAACGACCCTTTATAAATTTGATAACC-TCA
1 TTGAAATTTTGATAACCACCATTTATAAATTTGATAACCTTCA
* * * *
33184 TATGAAATTTTGGTAACCATCTTTTA-AAATTTTGATAACCTCCA
1 T-TGAAATTTTGATAACCACCATTTATAAA-TTTGATAACCTTCA
*
33228 TTAAAATTTTGA
1 TTGAAATTTTGA
33240 AAAATACCTC
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
42 6 0.08
43 70 0.89
44 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (43 bp):
TTGAAATTTTGATAACCACCATTTATAAATTTGATAACCTTCA
Found at i:33200 original size:21 final size:20
Alignment explanation
Indices: 33171--33239 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
33161 CCTTTATAAA
*
33171 TTTGATAACCTCATATGAAAT
1 TTTGATAACCTCAT-TAAAAT
* *
33192 TTTGGTAACCATCTTTTAAAAT
1 TTTGATAACC-TC-ATTAAAAT
33214 TTTGATAACCTCCATTAAAAT
1 TTTGATAACCT-CATTAAAAT
33235 TTTGA
1 TTTGA
33240 AAAATACCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 22 0.55
22 17 0.43
23 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (20 bp):
TTTGATAACCTCATTAAAAT
Found at i:33283 original size:22 final size:21
Alignment explanation
Indices: 33258--33350 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 21
33248 TCTTACGAGG
33258 TTTTGATAACAATCTTTTGTAA
1 TTTTGATAACAATC-TTTGTAA
* *
33280 TTTTGATAACTATCCATTGTAA
1 TTTTGATAACAAT-CTTTGTAA
* * * *
33302 TTTTTATAAACACTCTATGAAA
1 TTTTGAT-AACAATCTTTGTAA
* * *
33324 ATTTGGTAACAACCATTTGTAA
1 TTTTGATAACAATC-TTTGTAA
33346 TTTTG
1 TTTTG
33351 CTAGCAGCTC
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
21 5 0.10
22 42 0.81
23 5 0.10
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (21 bp):
TTTTGATAACAATCTTTGTAA
Found at i:35509 original size:23 final size:22
Alignment explanation
Indices: 35469--35514 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
35459 ATAAAGTAAT
35469 TAATTAATGTATTGATTAAAAA
1 TAATTAATGTATTGATTAAAAA
* * *
35491 TAATTATTAGTATTTATTATAAA
1 TAATTAAT-GTATTGATTAAAAA
35514 T
1 T
35515 TGTTCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TAATTAATGTATTGATTAAAAA
Found at i:37630 original size:123 final size:127
Alignment explanation
Indices: 37488--37739 Score: 395
Period size: 131 Copynumber: 2.0 Consensus size: 127
37478 CATTGTTTAA
* *
37488 ACTTTTATAGGTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAAGTAAATCTAATATCCTTATACT
37550 A-ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
37611 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAAGTAAATCTAATATCCTTATACC
1 ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAAGTAAATCTAATATCCTTATA-C
*
37676 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
37740 TTACAATTTT
Statistics
Matches: 116, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
123 52 0.45
124 3 0.03
125 2 0.02
127 2 0.02
131 57 0.49
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.49
Consensus pattern (127 bp):
ACTTTTACAGGTTTACTCAACTAAAAACTCTAATTTTATTTAAGTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:42863 original size:44 final size:44
Alignment explanation
Indices: 42800--42883 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
42790 AGAGGATAAT
*
42800 TGATCGGTCGTCAGCAATCATAAAAATAATCCCCACAAAATTTA
1 TGATCGGTCGTCAGCAATCACAAAAATAATCCCCACAAAATTTA
42844 TGATCGGTCGTCAGCAATCACAAAAATAATCCCCACAAAA
1 TGATCGGTCGTCAGCAATCACAAAAATAATCCCCACAAAA
42884 CCTAACTAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (44 bp):
TGATCGGTCGTCAGCAATCACAAAAATAATCCCCACAAAATTTA
Found at i:44505 original size:19 final size:18
Alignment explanation
Indices: 44481--44516 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
44471 CAAAATTGCT
44481 AAGTCCATATTTGAGTAAA
1 AAGTCCATATTTG-GTAAA
44500 AAGTCCATATTTGGTAA
1 AAGTCCATATTTGGTAA
44517 GTACACTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
AAGTCCATATTTGGTAAA
Found at i:45073 original size:12 final size:11
Alignment explanation
Indices: 45041--45070 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
45031 TCACAATAAT
45041 TAAATTTTAAA
1 TAAATTTTAAA
45052 TAAATTTTAAA
1 TAAATTTTAAA
45063 TAAATTTT
1 TAAATTTT
45071 TAACTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAATTTTAAA
Found at i:57870 original size:26 final size:27
Alignment explanation
Indices: 57826--57877 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
57816 TCGGTCACAT
57826 AATTGAAAAAATTGAAAGTTCAAGGGC
1 AATTGAAAAAATTGAAAGTTCAAGGGC
* *
57853 AATTG-AAAATTTGGAAGTTCAAGGG
1 AATTGAAAAAATTGAAAGTTCAAGGG
57878 TTACTTCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (27 bp):
AATTGAAAAAATTGAAAGTTCAAGGGC
Found at i:61216 original size:11 final size:11
Alignment explanation
Indices: 61199--61231 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
61189 TCTGGTGGAG
61199 GAAGAAG-AAA
1 GAAGAAGAAAA
61209 GAAAGAAGAAAA
1 G-AAGAAGAAAA
61221 GAAGAAGAAAA
1 GAAGAAGAAAA
61232 AAATCACGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 16 0.76
12 4 0.19
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAAA
Found at i:63530 original size:2 final size:2
Alignment explanation
Indices: 63523--63576 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
63513 ATATGTAGTA
63523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
63565 AT AT AT CT AT AT
1 AT AT AT AT AT AT
63577 TCCTAAGTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66791 original size:2 final size:2
Alignment explanation
Indices: 66784--66821 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
66774 ATAAATTGGA
66784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.