Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018979.1 Corchorus olitorius cultivar O-4 contig19012, 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: 119310
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:13449 original size:31 final size:31
Alignment explanation
Indices: 13414--13493 Score: 160
Period size: 31 Copynumber: 2.6 Consensus size: 31
13404 ATTAGGCTGT
13414 AATCTCAAATAAGGGCCCGAACTTTCATAAA
1 AATCTCAAATAAGGGCCCGAACTTTCATAAA
13445 AATCTCAAATAAGGGCCCGAACTTTCATAAA
1 AATCTCAAATAAGGGCCCGAACTTTCATAAA
13476 AATCTCAAATAAGGGCCC
1 AATCTCAAATAAGGGCCC
13494 CAAAACACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (31 bp):
AATCTCAAATAAGGGCCCGAACTTTCATAAA
Found at i:32423 original size:37 final size:37
Alignment explanation
Indices: 32382--32455 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
32372 CACTGCTTGT
*
32382 TCTTTTCCTTTTTCTACTTCTTGAGCCAACAAGCATC
1 TCTTTTCCCTTTTCTACTTCTTGAGCCAACAAGCATC
32419 TCTTTTCCCTTTTCTACTTCTTGAGCCAACAAGCATC
1 TCTTTTCCCTTTTCTACTTCTTGAGCCAACAAGCATC
32456 CAATGGATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.31, G:0.08, T:0.42
Consensus pattern (37 bp):
TCTTTTCCCTTTTCTACTTCTTGAGCCAACAAGCATC
Found at i:41958 original size:12 final size:12
Alignment explanation
Indices: 41941--41985 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
41931 CCACAAGGTA
41941 ATATATCCGTCG
1 ATATATCCGTCG
*
41953 ATATATCCATCG
1 ATATATCCGTCG
*
41965 ATATATCTGTTCG
1 ATATATCCG-TCG
41978 ATATATCC
1 ATATATCC
41986 ATGGATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (12 bp):
ATATATCCGTCG
Found at i:41981 original size:25 final size:24
Alignment explanation
Indices: 41941--41993 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
41931 CCACAAGGTA
41941 ATATATCCGTCGATATATCCATCG
1 ATATATCCGTCGATATATCCATCG
* *
41965 ATATATCTGTTCGATATATCCATGG
1 ATATATCCG-TCGATATATCCATCG
41990 ATAT
1 ATAT
41994 CTGTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (24 bp):
ATATATCCGTCGATATATCCATCG
Found at i:43796 original size:13 final size:13
Alignment explanation
Indices: 43778--43802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43768 TATGAACACC
43778 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
43791 AGAAAAAAAAAA
1 AGAAAAAAAAAA
43803 CCTTCAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:48637 original size:151 final size:142
Alignment explanation
Indices: 48428--48720 Score: 442
Period size: 151 Copynumber: 2.0 Consensus size: 142
48418 TTCATCACAA
*
48428 TTGGCATCTGGCTATCAGGAATGGAAGAAGCTAAATGGAGATTGGAGGCAAGAAATTAGCAAATT
1 TTGGCATCTGGCTATCAGGAAAGGAAGAAGCTAAATGGAGATTGGAGGCAAGAAATTAGCAAATT
* * *
48493 TATATAATAGGAAGATGATGCTTTGTAAATTGTAAGAATAAATTTAGAGGCAGGTTCCTAACCTA
66 TATATAACAGGAAGATGATGC----T---TTGTAAGAATAAATTTAGAGGCAGGCTCCTAACCAA
48558 TATCTGATATTAGCAATTT
124 TATCTGATATTAGCAATTT
48577 TTGGCATACTGGCTATCAGGAAAGGAAGAAGCTAAAATGGAGATTGGAGGCAAGAAATTAGCAAA
1 TTGGCAT-CTGGCTATCAGGAAAGGAAGAAGCT-AAATGGAGATTGGAGGCAAGAAATTAGCAAA
* **
48642 TTTATATGACAGGAAGATGATGCTTTGTAAGAATGCATTTAGAGGCAGGCTCCTAACCAATATCT
64 TTTATATAACAGGAAGATGATGCTTTGTAAGAATAAATTTAGAGGCAGGCTCCTAACCAATATCT
48707 GATATTAGCAATTT
129 GATATTAGCAATTT
48721 AGTACCAAAC
Statistics
Matches: 135, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
144 51 0.38
147 1 0.01
149 7 0.05
150 24 0.18
151 52 0.39
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (142 bp):
TTGGCATCTGGCTATCAGGAAAGGAAGAAGCTAAATGGAGATTGGAGGCAAGAAATTAGCAAATT
TATATAACAGGAAGATGATGCTTTGTAAGAATAAATTTAGAGGCAGGCTCCTAACCAATATCTGA
TATTAGCAATTT
Found at i:61430 original size:7 final size:7
Alignment explanation
Indices: 61418--61442 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61408 TTGAAGTTGG
61418 GGGATTT
1 GGGATTT
61425 GGGATTT
1 GGGATTT
61432 GGGATTT
1 GGGATTT
61439 GGGA
1 GGGA
61443 ATGGCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (7 bp):
GGGATTT
Found at i:63945 original size:6 final size:6
Alignment explanation
Indices: 63934--63961 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
63924 GAATAAAGTT
63934 GGATTG GGATTG GGATTG GGATTG GGAT
1 GGATTG GGATTG GGATTG GGATTG GGAT
63962 ATGCTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
GGATTG
Found at i:68629 original size:31 final size:31
Alignment explanation
Indices: 68591--68663 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
68581 AAACTTTATT
68591 CAATTAAGTCCCTAAAGTGAAGGGTTAGGAA
1 CAATTAAGTCCCTAAAGTGAAGGGTTAGGAA
68622 CAATTAAGTCCCTAAAGTGAAGGGTTAGGAA
1 CAATTAAGTCCCTAAAGTGAAGGGTTAGGAA
68653 CAATTAAGTCC
1 CAATTAAGTCC
68664 TTCCCTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (31 bp):
CAATTAAGTCCCTAAAGTGAAGGGTTAGGAA
Found at i:68980 original size:17 final size:18
Alignment explanation
Indices: 68958--68999 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
68948 AACTTTTTTT
*
68958 AGGAAAAAACAGAAAA-A
1 AGGAAAAAAAAGAAAAGA
68975 AGGAAAAAAAAGAAAAGA
1 AGGAAAAAAAAGAAAAGA
68993 A-GAAAAA
1 AGGAAAAA
69000 TCAAATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AGGAAAAAAAAGAAAAGA
Found at i:69465 original size:2 final size:2
Alignment explanation
Indices: 69458--69483 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69448 CTATTTTACA
69458 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
69484 TACATGCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71250 original size:24 final size:24
Alignment explanation
Indices: 71223--71271 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
71213 TTGTGATGAC
71223 TCACTACATGTGACAGCTTCATTA
1 TCACTACATGTGACAGCTTCATTA
71247 TCACTACATGTGACAGCTTCATTA
1 TCACTACATGTGACAGCTTCATTA
71271 T
1 T
71272 AACTTGAAGG
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:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (24 bp):
TCACTACATGTGACAGCTTCATTA
Found at i:85760 original size:27 final size:28
Alignment explanation
Indices: 85720--85785 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
85710 GATAAAGTTT
85720 TGAGAGAG-GAGCTATGAGTGTCCTTGG
1 TGAGAGAGAGAGCTATGAGTGTCCTTGG
* *
85747 TGAGAGAGAG-GCTATGGGTGTTCTTGG
1 TGAGAGAGAGAGCTATGAGTGTCCTTGG
85774 TGAGAGAGAGAG
1 TGAGAGAGAGAG
85786 ACTAAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.24, C:0.08, G:0.44, T:0.24
Consensus pattern (28 bp):
TGAGAGAGAGAGCTATGAGTGTCCTTGG
Found at i:93929 original size:32 final size:32
Alignment explanation
Indices: 93888--93949 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
93878 TAGCTCCTTG
93888 ACTATCATGTATACTTGATGCCTGTCCAATTA
1 ACTATCATGTATACTTGATGCCTGTCCAATTA
93920 ACTATCATGTATACTTGATGCCTGTCCAAT
1 ACTATCATGTATACTTGATGCCTGTCCAAT
93950 GGGGACTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (32 bp):
ACTATCATGTATACTTGATGCCTGTCCAATTA
Found at i:94050 original size:81 final size:82
Alignment explanation
Indices: 93915--94079 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 82
93905 ATGCCTGTCC
* * *
93915 AATTAACTATCATGTATACTTGATGCCTGTCCAATGGGGACTCATACACCATCACATTAATTTTC
1 AATTAACTATCATGTATACATGATGCCTGTCCAACGGGGACTCATACACCATCACATTAACTTTC
*
93980 TCCATTTGATGCT-CTT
66 TCCATTTAATGCTCCTT
*
93996 AATTAACTATCATGTATACATGATGCTTGTCCAACGGGGACTCA-ATCACCATCACATTAACTTT
1 AATTAACTATCATGTATACATGATGCCTGTCCAACGGGGACTCATA-CACCATCACATTAACTTT
94060 CTCCATTTAATGCTCCTT
65 CTCCATTTAATGCTCCTT
94078 AA
1 AA
94080 CTTGGGGATT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
80 1 0.01
81 71 0.92
82 5 0.06
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (82 bp):
AATTAACTATCATGTATACATGATGCCTGTCCAACGGGGACTCATACACCATCACATTAACTTTC
TCCATTTAATGCTCCTT
Found at i:96635 original size:15 final size:15
Alignment explanation
Indices: 96605--96646 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
96595 TTACTTTGTT
96605 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
96621 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
96636 TTGTTTTCTGT
1 TTGTTTTCTGT
96647 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:100703 original size:5 final size:5
Alignment explanation
Indices: 100693--100717 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
100683 GTAATCCAAA
100693 TTTGC TTTGC TTTGC TTTGC TTTGC
1 TTTGC TTTGC TTTGC TTTGC TTTGC
100718 CCCATGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.20, T:0.60
Consensus pattern (5 bp):
TTTGC
Found at i:108547 original size:54 final size:54
Alignment explanation
Indices: 108464--108584 Score: 233
Period size: 54 Copynumber: 2.2 Consensus size: 54
108454 AAACAGCCCC
*
108464 TTAGTGCCAATTTAGCAAGGGAAATAACCTTGTTCATGACAAGTAGAAGATAAG
1 TTAGTGCCAATTTAGCAAGGGAAAAAACCTTGTTCATGACAAGTAGAAGATAAG
108518 TTAGTGCCAATTTAGCAAGGGAAAAAACCTTGTTCATGACAAGTAGAAGATAAG
1 TTAGTGCCAATTTAGCAAGGGAAAAAACCTTGTTCATGACAAGTAGAAGATAAG
108572 TTAGTGCCAATTT
1 TTAGTGCCAATTT
108585 GCCTAACTTA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (54 bp):
TTAGTGCCAATTTAGCAAGGGAAAAAACCTTGTTCATGACAAGTAGAAGATAAG
Found at i:117966 original size:22 final size:22
Alignment explanation
Indices: 117941--118043 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
117931 TTGTCTCTGT
117941 ATGGTTATCAAAATTTCATAAG
1 ATGGTTATCAAAATTTCATAAG
* * * *
117963 ATGGTTATTATAATTTTATGAGG
1 ATGGTTATCAAAATTTCAT-AAG
*
117986 A-GGTTATCAAAATTCCAT-AG
1 ATGGTTATCAAAATTTCATAAG
* *
118006 TGTGGTTACCAAAATTTCATATAG
1 -ATGGTTATCAAAATTTCATA-AG
*
118030 A-AGTTATCAAAATT
1 ATGGTTATCAAAATT
118044 CCGTAGTGTG
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
20 1 0.02
22 55 0.90
23 3 0.05
24 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAAG
Found at i:118057 original size:22 final size:22
Alignment explanation
Indices: 117987--118065 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
117977 TTTATGAGGA
*
117987 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTCCATAGTGT
* *
118009 GGTTACCAAAATTTCATA-TAGA
1 GGTTACCAAAATTCCATAGT-GT
* * *
118031 AGTTATCAAAATTCCGTAGTGT
1 GGTTACCAAAATTCCATAGTGT
118053 GGTTACCAAAATT
1 GGTTACCAAAATT
118066 TCTTAGGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 1 0.02
22 43 0.96
23 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
GGTTACCAAAATTCCATAGTGT
Found at i:118176 original size:22 final size:22
Alignment explanation
Indices: 118151--118192 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
118141 GTTATCAAAG
118151 AGATTATCAA-AATTTCATAGCA
1 AGATTAT-AAGAATTTCATAGCA
118173 AGATTATAAGAATTTCATAG
1 AGATTATAAGAATTTCATAG
118193 TGTGGTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
AGATTATAAGAATTTCATAGCA
Found at i:118372 original size:23 final size:22
Alignment explanation
Indices: 118282--118565 Score: 129
Period size: 22 Copynumber: 12.9 Consensus size: 22
118272 AAAATTTGTA
**
118282 GTTATCAGGATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
118304 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAAGGAG
*
118326 TTTTATC-AAATATT-AT-AGGAAG
1 -GTTATCAAAAT-TTCATAAGG-AG
*
118348 GTTTATCAAAATTTCATAACGAG
1 G-TTATCAAAATTTCATAAGGAG
* *
118371 GTTATCACAATTTCAT-AGTGTG
1 GTTATCAAAATTTCATAAG-GAG
* *
118393 ATTATCAAAATTTCA-AAGTGTG
1 GTTATCAAAATTTCATAAG-GAG
* * *
118415 ATTA-CTAACAA-TTCATATGGAC
1 GTTATC-AA-AATTTCATAAGGAG
* * * *
118437 GTT-TTAAATTTTCATAA-CATT
1 GTTATCAAAATTTCATAAGGA-G
* * * **
118458 GTTATCAACATCTCATATTGTTG
1 GTTATCAAAATTTCATA-AGGAG
** *
118481 GTTATCAAAATTTCATTGGGAA
1 GTTATCAAAATTTCATAAGGAG
*
118503 GTTATCAAAATTTCATAATGAG
1 GTTATCAAAATTTCATAAGGAG
* *
118525 GTCT-TCAAAATTTCTTAGGGAG
1 GT-TATCAAAATTTCATAAGGAG
* *
118547 GTTAACGAAATTTCATAAG
1 GTTATCAAAATTTCATAAG
118566 AAAGTTAAAA
Statistics
Matches: 194, Mismatches: 48, Indels: 40
0.69 0.17 0.14
Matches are distributed among these distances:
20 2 0.01
21 16 0.08
22 139 0.72
23 35 0.18
24 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Done.