Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024892.1 Corchorus olitorius cultivar O-4 contig24925, 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: 41642
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2608 original size:17 final size:16
Alignment explanation
Indices: 2582--2616 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2572 TAATTTGGAA
2582 TTAAAATTTTCTCATT
1 TTAAAATTTTCTCATT
*
2598 TTAATAATTTTTTCATT
1 TTAA-AATTTTCTCATT
2615 TT
1 TT
2617 TTTTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAAAATTTTCTCATT
Found at i:4881 original size:2 final size:2
Alignment explanation
Indices: 4876--4909 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4866 CTACTAATTA
*
4876 AT AT AT AT AT AT AT AT AT CT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4910 AGTCTAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5182 original size:39 final size:40
Alignment explanation
Indices: 5126--5206 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
5116 TTTAATTCCT
5126 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
5166 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
5205 AT
1 AT
5207 TCTTAGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:5232 original size:24 final size:23
Alignment explanation
Indices: 5197--5242 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
5187 AATACTTACA
5197 TTAATTAAATTCTTAGATATTTT
1 TTAATTAAATTCTTAGATATTTT
*
5220 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
5243 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGATATTTT
Found at i:6284 original size:36 final size:36
Alignment explanation
Indices: 6237--6306 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
6227 AAGATTTTGG
* *
6237 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
6273 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
6307 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:8259 original size:10 final size:10
Alignment explanation
Indices: 8244--8274 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
8234 GATAATCTTA
8244 TTCTTTTTTT
1 TTCTTTTTTT
8254 TTCTTTTTTT
1 TTCTTTTTTT
8264 TT-TTTTTTT
1 TTCTTTTTTT
8273 TT
1 TT
8275 GGCATCAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:9700 original size:106 final size:104
Alignment explanation
Indices: 9529--9789 Score: 416
Period size: 106 Copynumber: 2.5 Consensus size: 104
9519 AGTTTAGCCT
* *
9529 TAATTTCACTAGGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGC-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
9594 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
9636 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* *
9701 ATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
9740 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
9790 TAGAAAAATT
Statistics
Matches: 146, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 44 0.30
104 36 0.25
106 48 0.33
107 18 0.12
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:10579 original size:1 final size:1
Alignment explanation
Indices: 10573--10619 Score: 94
Period size: 1 Copynumber: 47.0 Consensus size: 1
10563 GCAGCTAGTA
10573 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10620 CTGTTTGTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11073 original size:2 final size:2
Alignment explanation
Indices: 11066--11102 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11056 AATTATTGGA
11066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11103 GGCAAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12783 original size:26 final size:26
Alignment explanation
Indices: 12747--12800 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
12737 AATCCGCCTT
*
12747 AGCCATATTTTTAGATTTTTTTATGA
1 AGCCATATTTTTAGATTTTGTTATGA
12773 AGCCATATTTTTAGATTTTGTTATGA
1 AGCCATATTTTTAGATTTTGTTATGA
12799 AG
1 AG
12801 TAGTGTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (26 bp):
AGCCATATTTTTAGATTTTGTTATGA
Found at i:13364 original size:41 final size:41
Alignment explanation
Indices: 13318--13412 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
13308 AAATTACCTT
* *
13318 TGACACCACAAGTTGTCACTTTGGTAAATTAAAATTACTGC
1 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATGACTGC
* **
13359 TGACACTAGAAGTTGTCACTTTGGTAAATTAAAATGACTTT
1 TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATGACTGC
13400 TGACACCAGAAGT
1 TGACACCAGAAGT
13413 GTTACTCCAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (41 bp):
TGACACCAGAAGTTGTCACTTTGGTAAATTAAAATGACTGC
Found at i:16650 original size:48 final size:48
Alignment explanation
Indices: 16589--16685 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
16579 ATTAAGAAAT
16589 AGTATAGAAAGGATCCCATCGACCCATGTGTGTTTATCAAGAAATTGA
1 AGTATAGAAAGGATCCCATCGACCCATGTGTGTTTATCAAGAAATTGA
16637 AGTATAGAAAGGATCCCATCGACCCATGTGTGTTTATCAAGAAATTGA
1 AGTATAGAAAGGATCCCATCGACCCATGTGTGTTTATCAAGAAATTGA
16685 A
1 A
16686 AACCGGATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (48 bp):
AGTATAGAAAGGATCCCATCGACCCATGTGTGTTTATCAAGAAATTGA
Found at i:18080 original size:11 final size:11
Alignment explanation
Indices: 18060--18090 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
18050 AAGATTTCAA
18060 CTGAAGATTAT
1 CTGAAGATTAT
*
18071 CTGGAGATTAT
1 CTGAAGATTAT
18082 CTGAAGATT
1 CTGAAGATT
18091 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:19336 original size:18 final size:18
Alignment explanation
Indices: 19313--19357 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
19303 AAATTTATTA
19313 ATTATTAAATAAATAATC
1 ATTATTAAATAAATAATC
*** *
19331 ATTATTTTCTGAATAATC
1 ATTATTAAATAAATAATC
19349 ATTATTAAA
1 ATTATTAAA
19358 ATCGTCATCT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTATTAAATAAATAATC
Found at i:22730 original size:2 final size:2
Alignment explanation
Indices: 22723--22748 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22713 ACATGCATTA
22723 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
22749 TTAATGACAA
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:23841 original size:27 final size:27
Alignment explanation
Indices: 23801--23915 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
23791 AGGTGACTGC
* *
23801 TGGTGGGCCTAGTGGGTCTGAAAATCT
1 TGGTGGTCCAAGTGGGTCTGAAAATCT
* *
23828 TGGTGGTCTAAGTGGGGCTGAAAATCT
1 TGGTGGTCCAAGTGGGTCTGAAAATCT
* *
23855 TGGTGGTCCAAG-GGTGTCTGACAATGT
1 TGGTGGTCCAAGTGG-GTCTGAAAATCT
* * *
23882 TGGTGGGCCAAGAGTGG-CTGAAAATGT
1 TGGTGGTCCAAGTG-GGTCTGAAAATCT
23909 TGGTGGT
1 TGGTGGT
23916 GGGGCAAGTG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.03
27 69 0.93
28 2 0.03
29 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.39, T:0.29
Consensus pattern (27 bp):
TGGTGGTCCAAGTGGGTCTGAAAATCT
Found at i:27986 original size:106 final size:105
Alignment explanation
Indices: 27759--28019 Score: 339
Period size: 106 Copynumber: 2.5 Consensus size: 105
27749 AATTTTTCTA
* ** *
27759 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGGCTAAACTTAGTG-AATTAGTTAAATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTAAATATTTTA
* * * *
27822 TTTCTAAAATCCTATAATAATATTATTAATTACGGAATTT
66 TTTCTAAAACCCTATAACAATATTATAAATTACGAAATTT
* ***
27862 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTGAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTAAATATTTTA
* **
27927 TTTCTAAAACCCTTTAACAATAAATT-TAAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATAAATTACGAAATTT
*
27968 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
28020 AGACTAAACT
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
103 27 0.20
104 13 0.09
105 33 0.24
106 61 0.45
107 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTAAATATTTTA
TTTCTAAAACCCTATAACAATATTATAAATTACGAAATTT
Found at i:36205 original size:33 final size:33
Alignment explanation
Indices: 36159--36240 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
36149 GCAGTTGCAA
*
36159 AGGGAGAGAGAGGCTGAGGCTGCTCGGATGTAT
1 AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
36192 AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
1 AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
36225 AGGGAGAGGGAGGCTG
1 AGGGAGAGGGAGGCTG
36241 CTGATGGTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.23, C:0.11, G:0.50, T:0.16
Consensus pattern (33 bp):
AGGGAGAGGGAGGCTGAGGCTGCTCGGATGTAT
Found at i:38308 original size:10 final size:10
Alignment explanation
Indices: 38295--38336 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
38285 TATATTTTTG
*
38295 GGATTTGTAT
1 GGATTTTTAT
38305 GGATTTTTTAT
1 GGA-TTTTTAT
*
38316 GTATTTTTAT
1 GGATTTTTAT
38326 GGATTTTTAT
1 GGATTTTTAT
38336 G
1 G
38337 TATATTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:38321 original size:21 final size:20
Alignment explanation
Indices: 38297--38339 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
38287 TATTTTTGGG
38297 ATTTGTATGGATTTTTTATGT
1 ATTTGTATGGA-TTTTTATGT
*
38318 ATTTTTATGGATTTTTATGT
1 ATTTGTATGGATTTTTATGT
38338 AT
1 AT
38340 ATTGGGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (20 bp):
ATTTGTATGGATTTTTATGT
Done.