Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015859.1 Corchorus olitorius cultivar O-4 contig15892, 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: 14469
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6046 original size:21 final size:20
Alignment explanation
Indices: 6017--6065 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
6007 ATAAATAAAT
*
6017 AAATGAAAATGAAAATGAAGG-
1 AAATAAAAATGAAAA--AAGGA
6038 AAATAAAAAATGAAAAAAGGA
1 AAAT-AAAAATGAAAAAAGGA
6059 AAATAAA
1 AAATAAA
6066 GGCACTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 10 0.40
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATAAAAATGAAAAAAGGA
Found at i:6057 original size:20 final size:22
Alignment explanation
Indices: 6022--6065 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6012 TAAATAAATG
6022 AAAATGAAAATGAAGG-AAATAA
1 AAAATGAAAA-GAAGGAAAATAA
6044 AAAATGAAAA-AAGGAAAATAA
1 AAAATGAAAAGAAGGAAAATAA
6065 A
1 A
6066 GGCACTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 7 0.33
22 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (22 bp):
AAAATGAAAAGAAGGAAAATAA
Found at i:6456 original size:23 final size:23
Alignment explanation
Indices: 6430--6502 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
6420 AGTCCCCTCC
*
6430 ATCAAGAAAT-TCAAATAAAAAAA
1 ATCAAAAAATATCAAA-AAAAAAA
6453 ATCAAAAAATATCAAAAAAAAAA
1 ATCAAAAAATATCAAAAAAAAAA
* **
6476 A-CAAACAA-ATCAAAATCAAAA
1 ATCAAAAAATATCAAAAAAAAAA
6497 ATCAAA
1 ATCAAA
6503 TCAAATCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 12 0.27
22 10 0.23
23 17 0.39
24 5 0.11
ACGTcount: A:0.73, C:0.12, G:0.01, T:0.14
Consensus pattern (23 bp):
ATCAAAAAATATCAAAAAAAAAA
Found at i:6473 original size:24 final size:23
Alignment explanation
Indices: 6430--6476 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
6420 AGTCCCCTCC
* *
6430 ATCAAGAAATTCAAATAAAAAAA
1 ATCAAAAAATTCAAAAAAAAAAA
6453 ATCAAAAAATATCAAAAAAAAAAA
1 ATCAAAAAAT-TCAAAAAAAAAAA
6477 CAAACAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (23 bp):
ATCAAAAAATTCAAAAAAAAAAA
Found at i:6491 original size:6 final size:6
Alignment explanation
Indices: 6482--6519 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
6472 AAAAACAAAC
6482 AAATCA AAATCAA AAATC- AAATC- AAATCA AAATCA AAA
1 AAATCA AAATC-A AAATCA AAATCA AAATCA AAATCA AAA
6520 GAGAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.33
6 14 0.47
7 6 0.20
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATCA
Found at i:6507 original size:23 final size:22
Alignment explanation
Indices: 6449--6519 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
6439 TTCAAATAAA
* *
6449 AAAAATCAAAAAATATCAAAA-A
1 AAAAATCAAACAA-ATCAAAATC
*
6471 AAAAAACAAACAAATCAAAATC
1 AAAAATCAAACAAATCAAAATC
6493 AAAAATCAAATCAAATCAAAATC
1 AAAAATCAAA-CAAATCAAAATC
6516 AAAA
1 AAAA
6520 GAGAATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 7 0.16
22 20 0.47
23 16 0.37
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAAATCAAACAAATCAAAATC
Found at i:7255 original size:50 final size:50
Alignment explanation
Indices: 7107--7255 Score: 208
Period size: 50 Copynumber: 3.0 Consensus size: 50
7097 GTTTTATAAC
* * *
7107 AAGATTTCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
1 AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
* *
7157 AAAATTGCTTTCCATTTGTGAGTTCAAGATTAAAATTCGCTTTTCAAAGT
1 AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
* * * * *
7207 AAGATTGCATTCCAGTTGTGAGTCCAATATCAAAATTCGTTTTTCAAAG
1 AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
7256 GGCATTTAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (50 bp):
AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
Found at i:7933 original size:50 final size:50
Alignment explanation
Indices: 7858--7984 Score: 236
Period size: 50 Copynumber: 2.5 Consensus size: 50
7848 CGAATGTTTC
7858 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
7908 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
7958 GACTTTTCCACAAGCCAAAATCGTTTC
1 GGCTTTTCCACAAGCCAAACTCGTTTC
7985 AATTATCAAC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:8004 original size:40 final size:41
Alignment explanation
Indices: 7943--8025 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 41
7933 TCCATACGAG
7943 TCAATTATCAACATAGACTTTTCCACAAGCCA-AAATCGTT
1 TCAATTATCAACATAGACTTTTCCACAAGCCACAAATCGTT
* * * *
7983 TCAATTATCAACATGGGCTTTTCCATAAGCCACAACTCGTT
1 TCAATTATCAACATAGACTTTTCCACAAGCCACAAATCGTT
8024 TC
1 TC
8026 CATACGATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
40 29 0.76
41 9 0.24
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (41 bp):
TCAATTATCAACATAGACTTTTCCACAAGCCACAAATCGTT
Found at i:8095 original size:35 final size:34
Alignment explanation
Indices: 8047--8774 Score: 708
Period size: 35 Copynumber: 21.1 Consensus size: 34
8037 TTACCATCTT
* * * *
8047 CTCAGATGGCTCGGGGTAGCATCTTCAAAGTTATA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAATGA-A
8082 CTCAGATGACTCGGTGTAGCATCTTCAAAGATGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAA-ATGAA
*
8117 -TCAGATGACTCGGTGTAGCATCTTCAAGAATGAC
1 CTCAGATGACTCGGTGTAGCATCTTCAA-AATGAA
** *
8151 CTTGGATGACTCTGTGTAGCATCTTCAAAGATGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAA-ATGAA
* *
8186 TTCAAATGACTCGGTGTAGCATCTTCAAAAATGAA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
* *
8221 TTCAGATGACTCGGTGTAGCATCTTCAAAAATGAT
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
* *
8256 CCCTGATGACTCGGTGTAGCATCTTCAAAAATGAA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
* *
8291 TTCAGATGACTCGGTGTAGCATCTTCAAAAATGAT
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
* * * * *
8326 CCCGGGTGACTCGGCGTATCATCTTCAAAAATGAA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
* *
8361 TTCAGATGACTCGGTGTAGCATCTTCAAAAATGGA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
*
8396 TTCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
8431 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAATGAA
* *
8466 CTCAGATGACTCGGTGTAGCATCTTTAAAAATGAT
1 CTCAGATGACTCGGTGTAGCATC-TTCAAAATGAA
*
8501 CTCAGATGACACGGTGTAGCATCTTC-AAA-G-A
1 CTCAGATGACTCGGTGTAGCATCTTCAAAATGAA
*
8532 -TCAGGATGACTCGGTGTAGCATCTTCAATATGAA
1 CTCA-GATGACTCGGTGTAGCATCTTCAAAATGAA
*
8566 CTCAGATGACTCGGTGTAACATCTTCAAAGATGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAA-ATGAA
* * * * *
8601 TTCAGATTACTTGGTGTAGCATCTTCAATATGGA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAATGAA
* * * * *
8635 CTCA-CTGGGCTCGATGCAGCAAATC-TCCAAAT-AGA
1 CTCAGAT-GACTCGGTGTAGC--ATCTTCAAAATGA-A
* * *
8670 -TCAGGATGACCCGGTGTAGCATCTTCAATATGGA
1 CTCA-GATGACTCGGTGTAGCATCTTCAAAATGAA
* * * *
8704 CTCAG-TGGGCTCGATGCAGCAAATC-TCCAAAT-AGA
1 CTCAGAT-GACTCGGTGTAGC--ATCTTCAAAATGA-A
* *
8739 -TCAGGATGACCCGGTGTAGCATCTTCAATATGAA
1 CTCA-GATGACTCGGTGTAGCATCTTCAAAATGAA
8773 CT
1 CT
8775 TGTGTTTCTT
Statistics
Matches: 577, Mismatches: 86, Indels: 60
0.80 0.12 0.08
Matches are distributed among these distances:
30 3 0.01
31 21 0.04
32 3 0.01
33 12 0.02
34 101 0.18
35 422 0.73
36 15 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (34 bp):
CTCAGATGACTCGGTGTAGCATCTTCAAAATGAA
Found at i:8273 original size:105 final size:104
Alignment explanation
Indices: 8047--8628 Score: 784
Period size: 105 Copynumber: 5.6 Consensus size: 104
8037 TTACCATCTT
* * * * *
8047 CTCAGATGGCTCGGGGTAGCATCTTC-AAAGTTATACTCAGATGACTCGGTGTAGCATCTTCAAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGA-ATTCAGATGACTCGGTGTAGCATCTTCAAA
* * *
8111 GATGAATCAGATGACTCGGTGTAGCATCTTCAAGAATGAC
65 AATGAATCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
** * * *
8151 CTTGGATGACTCTGTGTAGCATCTTCAAAGATGAATTCAAATGACTCGGTGTAGCATCTTCAAAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
*
8216 ATGAATTCAGATGACTCGGTGTAGCATCTTCAAAAATGAT
66 ATGAA-TCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
* *
8256 CCCTGATGACTCGGTGTAGCATCTTCAAAAATGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
* * * *
8321 ATG-ATCCCGGGTGACTCGGCGTATCATCTTCAAAAATGAA
66 ATGAAT--CAGATGACTCGGTGTAGCATCTTCAAAAATGAA
* *
8361 TTCAGATGACTCGGTGTAGCATCTTCAAAAATGGATTCAGATGACTCGGTGTAGCATCTTCAAAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
8426 ATGAACTCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
66 ATGAA-TCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
* *
8466 CTCAGATGACTCGGTGTAGCATCTTTAAAAATG-ATCTCAGATGACACGGTGTAGCATCTTC--A
1 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAAT-TCAGATGACTCGGTGTAGCATCTTCAAA
*
8528 AA-G-ATCAGGATGACTCGGTGTAGCATCTTC-AATATGAA
65 AATGAATCA-GATGACTCGGTGTAGCATCTTCAAAAATGAA
* * * *
8566 CTCAGATGACTCGGTGTAACATCTTCAAAGATGAATTCAGATTACTTGGTGTAGCATCTTCAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAATTCAGATGACTCGGTGTAGCATCTTCAA
8629 TATGGACTCA
Statistics
Matches: 425, Mismatches: 42, Indels: 24
0.87 0.09 0.05
Matches are distributed among these distances:
100 62 0.15
101 25 0.06
102 1 0.00
103 4 0.01
104 57 0.13
105 274 0.64
106 1 0.00
107 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (104 bp):
CTCAGATGACTCGGTGTAGCATCTTCAAAAATGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
ATGAATCAGATGACTCGGTGTAGCATCTTCAAAAATGAA
Found at i:8686 original size:69 final size:69
Alignment explanation
Indices: 8613--8770 Score: 307
Period size: 69 Copynumber: 2.3 Consensus size: 69
8603 CAGATTACTT
8613 GGTGTAGCATCTTCAATATGGACTCACTGGGCTCGATGCAGCAAATCTCCAAATAGATCAGGATG
1 GGTGTAGCATCTTCAATATGGACTCACTGGGCTCGATGCAGCAAATCTCCAAATAGATCAGGATG
8678 ACCC
66 ACCC
*
8682 GGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGATGCAGCAAATCTCCAAATAGATCAGGATG
1 GGTGTAGCATCTTCAATATGGACTCACTGGGCTCGATGCAGCAAATCTCCAAATAGATCAGGATG
8747 ACCC
66 ACCC
8751 GGTGTAGCATCTTCAATATG
1 GGTGTAGCATCTTCAATATG
8771 AACTTGTGTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 88 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (69 bp):
GGTGTAGCATCTTCAATATGGACTCACTGGGCTCGATGCAGCAAATCTCCAAATAGATCAGGATG
ACCC
Found at i:9034 original size:28 final size:28
Alignment explanation
Indices: 9003--9079 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
8993 TTAGGATCAA
*
9003 CTAGGGGCATTTTGGTGATTTTCAAAAT
1 CTAGGGGCATTTTGGTCATTTTCAAAAT
* * *
9031 CTAGGGGCATTTTGGTCATTTGCACATT
1 CTAGGGGCATTTTGGTCATTTTCAAAAT
9059 C-AGGGGCATTTTGGTCATTTT
1 CTAGGGGCATTTTGGTCATTTT
9080 AAGTTCACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.40
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTCAAAAT
Found at i:9315 original size:21 final size:21
Alignment explanation
Indices: 9289--9333 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
9279 AGCAATCCTC
9289 CATCAACTTAACATTAGTTGT
1 CATCAACTTAACATTAGTTGT
*
9310 CATCAATTTAACATTAGTTGT
1 CATCAACTTAACATTAGTTGT
9331 CAT
1 CAT
9334 TTGCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (21 bp):
CATCAACTTAACATTAGTTGT
Found at i:9403 original size:60 final size:58
Alignment explanation
Indices: 9310--9424 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 58
9300 CATTAGTTGT
9310 CATCAATTTAACATTAGTTGTCATTTGCAAAAATGTTTTTATTAGTGGCATTTAGAACTC
1 CATCAATTTAACATTAGTTGTCATTTGCAAAAATG-TTTT-TTAGTGGCATTTAGAACTC
*
9370 CATCAATTTAACATTAGTTGTCATTTGCAAAAATGTTTTTTAGTTGCATTTAGAA
1 CATCAATTTAACATTAGTTGTCATTTGCAAAAATGTTTTTTAGTGGCATTTAGAA
9425 TATAAGTATG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
58 15 0.28
59 4 0.07
60 35 0.65
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (58 bp):
CATCAATTTAACATTAGTTGTCATTTGCAAAAATGTTTTTTAGTGGCATTTAGAACTC
Found at i:11737 original size:15 final size:15
Alignment explanation
Indices: 11707--11746 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
11697 TTCCTTTGCT
*
11707 TTGTTTTCAAGTTTAA
1 TTGTTTTC-TGTTTAA
11723 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
11738 TTGCTTTCT
1 TTGTTTTCT
11747 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:14010 original size:16 final size:16
Alignment explanation
Indices: 13989--14019 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13979 TTTCTTTGCA
13989 TGCTTTGATTGATTGT
1 TGCTTTGATTGATTGT
14005 TGCTTTGATTGATTG
1 TGCTTTGATTGATTG
14020 CCTATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.26, T:0.55
Consensus pattern (16 bp):
TGCTTTGATTGATTGT
Done.