Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015551.1 Corchorus olitorius cultivar O-4 contig15584, 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: 35026
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:241 original size:22 final size:22
Alignment explanation
Indices: 216--257 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
206 AATTTTGTTT
* *
216 ACCTCCCTAAGGAATTTTGAAG
1 ACCTCACTAAGAAATTTTGAAG
*
238 ACCTCACTATGAAATTTTGA
1 ACCTCACTAAGAAATTTTGA
258 TAACTAACAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (22 bp):
ACCTCACTAAGAAATTTTGAAG
Found at i:307 original size:22 final size:22
Alignment explanation
Indices: 281--352 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
271 GAGATATTTA
*
281 ATAACCTCCATATTATATATTG
1 ATAACCTCAATATTATATATTG
* ** * * *
303 ATAACCACGTTATCA-AAATTTA
1 ATAACCTCAATATTATATA-TTG
325 ATAACCTCAATATTATATATTG
1 ATAACCTCAATATTATATATTG
347 ATAACC
1 ATAACC
353 ACATTATCAA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
ATAACCTCAATATTATATATTG
Found at i:307 original size:46 final size:44
Alignment explanation
Indices: 254--383 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 44
244 CTATGAAATT
* * *
254 TTGATAACTAACACTATGAGATATTTAATAACCTCCATATTATATA
1 TTGATAAC-AACACTATCA-AAATTTAATAACCTCAATATTATATA
* **
300 TTGATAACCACGTTATCAAAATTTAATAACCTCAATATTATATA
1 TTGATAACAACACTATCAAAATTTAATAACCTCAATATTATATA
* * *
344 TTGATAACCACATTATCAAAATTTAAAAACCTTCAATATT
1 TTGATAACAACACTATCAAAATTTAATAACC-TCAATATT
384 GCATATATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
44 53 0.71
45 14 0.19
46 8 0.11
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (44 bp):
TTGATAACAACACTATCAAAATTTAATAACCTCAATATTATATA
Found at i:332 original size:44 final size:44
Alignment explanation
Indices: 276--383 Score: 180
Period size: 44 Copynumber: 2.4 Consensus size: 44
266 ACTATGAGAT
* *
276 ATTTAATAACCTCCATATTATATATTGATAACCACGTTATCAAA
1 ATTTAATAACCTCAATATTATATATTGATAACCACATTATCAAA
320 ATTTAATAACCTCAATATTATATATTGATAACCACATTATCAAA
1 ATTTAATAACCTCAATATTATATATTGATAACCACATTATCAAA
*
364 ATTTAAAAACCTTCAATATT
1 ATTTAATAACC-TCAATATT
384 GCATATATAT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 52 0.87
45 8 0.13
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.37
Consensus pattern (44 bp):
ATTTAATAACCTCAATATTATATATTGATAACCACATTATCAAA
Found at i:3347 original size:29 final size:30
Alignment explanation
Indices: 3298--3358 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
3288 GTTCTAATTA
* *
3298 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
3328 ATGTATAAATAT-GATTATTCAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
3357 AT
1 AT
3359 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:13486 original size:20 final size:20
Alignment explanation
Indices: 13463--13516 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
13453 TTTTTCTTAA
13463 CCAAAAATTTTTTGGGGTAG
1 CCAAAAATTTTTTGGGGTAG
*
13483 CCAACAATTTTTTTGGGGTAG
1 CCAA-AAATTTTTTGGGGTAG
*
13504 CCAACAATTTTTT
1 CCAAAAATTTTTT
13517 TTTCTAGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.39
Consensus pattern (20 bp):
CCAAAAATTTTTTGGGGTAG
Found at i:13518 original size:22 final size:21
Alignment explanation
Indices: 13470--13517 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
13460 TAACCAAAAA
13470 TTTTTTGGGGTAGCCAACAAT
1 TTTTTTGGGGTAGCCAACAAT
13491 TTTTTTGGGGTAGCCAACAAT
1 TTTTTTGGGGTAGCCAACAAT
13512 TTTTTT
1 TTTTTT
13518 TTCTAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (21 bp):
TTTTTTGGGGTAGCCAACAAT
Found at i:19167 original size:7 final size:7
Alignment explanation
Indices: 19157--19185 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
19147 TGAACTGATG
19157 TCTTCAC
1 TCTTCAC
19164 TCTTCAC
1 TCTTCAC
19171 TCTTCAC
1 TCTTCAC
19178 TCTTCAC
1 TCTTCAC
19185 T
1 T
19186 TTGAATGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (7 bp):
TCTTCAC
Found at i:19662 original size:2 final size:2
Alignment explanation
Indices: 19655--19684 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19645 ATTAAGTACT
*
19655 AC AC AC AC AC AC AC AC AC AC AC AG AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19685 TAACATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:22204 original size:38 final size:37
Alignment explanation
Indices: 22162--22233 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
22152 GTGGTATTCC
*
22162 AGTTAGAAT-ATGATTTTCCAAAAAAAAGGATGTTTACT
1 AGTTAGAATAATAATTTTCC--AAAAAAGGATGTTTACT
*
22200 AGTTAGGATAATAATTTTCCAAAAAAGGATGTTT
1 AGTTAGAATAATAATTTTCCAAAAAAGGATGTTT
22234 TCTATTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 14 0.45
38 8 0.26
39 9 0.29
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (37 bp):
AGTTAGAATAATAATTTTCCAAAAAAGGATGTTTACT
Found at i:23164 original size:48 final size:48
Alignment explanation
Indices: 23102--23197 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
23092 CTGATGCCGA
23102 AGGTCATCATAAGCATCACCACCATCATGGTGGTGGTGGTGATGGTGG
1 AGGTCATCATAAGCATCACCACCATCATGGTGGTGGTGGTGATGGTGG
* *
23150 AGGTCATCATAAGCATCATCACCATCATGGTGGTGGTGGTGGTGGTGG
1 AGGTCATCATAAGCATCACCACCATCATGGTGGTGGTGGTGATGGTGG
23198 TGGTGGTGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (48 bp):
AGGTCATCATAAGCATCACCACCATCATGGTGGTGGTGGTGATGGTGG
Found at i:23183 original size:3 final size:3
Alignment explanation
Indices: 23177--23227 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
23167 ATCACCATCA
*
23177 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGA TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
23225 TGG
1 TGG
23228 GGGTCATCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.02, C:0.00, G:0.65, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:26615 original size:27 final size:27
Alignment explanation
Indices: 26584--26638 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
26574 TCTAGAATTT
26584 TTTGAAAATATACAAATCTAAACTCCA
1 TTTGAAAATATACAAATCTAAACTCCA
*
26611 TTTGAAAATATACAAATCTGAACTCCA
1 TTTGAAAATATACAAATCTAAACTCCA
26638 T
1 T
26639 GTTATGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.31
Consensus pattern (27 bp):
TTTGAAAATATACAAATCTAAACTCCA
Found at i:26776 original size:21 final size:21
Alignment explanation
Indices: 26752--26814 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
26742 AGAAGGATAC
26752 AACAGAGAATGAAGAAGGGAG
1 AACAGAGAATGAAGAAGGGAG
* * *
26773 AACAGAGGGA-GAAGAA--TAC
1 AACAGA-GAATGAAGAAGGGAG
*
26792 AATAGAGAATGAAGAAGGGAG
1 AACAGAGAATGAAGAAGGGAG
26813 AA
1 AA
26815 GAAAACGCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.54, C:0.05, G:0.35, T:0.06
Consensus pattern (21 bp):
AACAGAGAATGAAGAAGGGAG
Found at i:26877 original size:20 final size:20
Alignment explanation
Indices: 26852--26891 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
26842 TATTTTGGCA
26852 TGTCGTTTTTCCCCTGGTTC
1 TGTCGTTTTTCCCCTGGTTC
26872 TGTCGTTTTTCCCCTGGTTC
1 TGTCGTTTTTCCCCTGGTTC
26892 GTTGAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.30, G:0.20, T:0.50
Consensus pattern (20 bp):
TGTCGTTTTTCCCCTGGTTC
Found at i:27275 original size:15 final size:15
Alignment explanation
Indices: 27255--27287 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
27245 TTAGCCATTC
27255 TTTCTTTTCTTTTT-T
1 TTTCTTTT-TTTTTAT
27270 TTTCTTTTTTTTTAT
1 TTTCTTTTTTTTTAT
27285 TTT
1 TTT
27288 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTCTTTTTTTTTAT
Found at i:27276 original size:19 final size:18
Alignment explanation
Indices: 27252--27290 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
27242 TATTTAGCCA
27252 TTCTTTCTTTTCTT-TTTTT
1 TTCTTT-TTTT-TTATTTTT
27271 TTCTTTTTTTTTATTTTT
1 TTCTTTTTTTTTATTTTT
27289 TT
1 TT
27291 AAAATTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 11 0.58
19 6 0.32
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (18 bp):
TTCTTTTTTTTTATTTTT
Found at i:27280 original size:11 final size:10
Alignment explanation
Indices: 27259--27290 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
27249 CCATTCTTTC
27259 TTTTCTTTTT
1 TTTTCTTTTT
27269 TTTTCTTTTT
1 TTTTCTTTTT
*
27279 TTTTATTTTT
1 TTTTCTTTTT
27289 TT
1 TT
27291 AAAATTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:33933 original size:46 final size:46
Alignment explanation
Indices: 33845--33933 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
33835 CTAATTTTAT
* * *
33845 AGAGTGATTCCCAAAAGAGTGCTCTCCATGGAGAGTCATTCCAATG
1 AGAGTGATTCCCAAAAGAGTACTCTCCATGAAAAGTCATTCCAATG
* * * *
33891 AGAGTGATTCCCAAGAGAGTACTTTTCATGAAAAGTCTTTCCA
1 AGAGTGATTCCCAAAAGAGTACTCTCCATGAAAAGTCATTCCA
33934 TACTCCCCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (46 bp):
AGAGTGATTCCCAAAAGAGTACTCTCCATGAAAAGTCATTCCAATG
Found at i:34926 original size:4 final size:4
Alignment explanation
Indices: 34909--35026 Score: 78
Period size: 4 Copynumber: 31.0 Consensus size: 4
34899 GAAAAAGGGA
**
34909 AAAG AAA- AAA- AAAG AAAG AGGAA- AAAG ATAA- AAAG AAA- AGGG AAAG
1 AAAG AAAG AAAG AAAG AAAG A--AAG AAAG A-AAG AAAG AAAG AAAG AAAG
* *
34955 -AA- AAAG AAAG -AAG AAAG AAAG AAGG AAA- AGAA- AAAG AAA- AAGG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG
34998 AAAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 -AAAG AAAG AAAG AAAG AAAG AAAG AAAG
Statistics
Matches: 92, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
3 23 0.25
4 61 0.66
5 6 0.07
6 2 0.02
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:34932 original size:30 final size:29
Alignment explanation
Indices: 34899--35017 Score: 95
Period size: 30 Copynumber: 3.9 Consensus size: 29
34889 AAAAAATGGG
*
34899 GAAAAAGGGAAAAGAAA-AAAAAAGAAAGAG
1 GAAAAA-GGAAAAGAAAGAAAAAAGAAA-AA
*
34929 GAAAAA-GATAA-AAAGAAAAGGGAAAGAAAAA
1 GAAAAAGGAAAAGAAAG-AAA---AAAGAAAAA
34960 GAAAGAA-G-AAAGAAAGAAGGAAAAGAAAAA
1 GAAA-AAGGAAAAGAAAGAA--AAAAGAAAAA
34990 GAAAAAGGAAAAGAAAGAAAGAAAGAAA
1 GAAAAAGGAAAAGAAAGAAA-AAAGAAA
35018 GAAAGAAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 24
0.73 0.03 0.24
Matches are distributed among these distances:
27 3 0.04
28 4 0.05
29 6 0.08
30 27 0.36
31 19 0.26
32 14 0.19
33 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (29 bp):
GAAAAAGGAAAAGAAAGAAAAAAGAAAAA
Found at i:34947 original size:36 final size:37
Alignment explanation
Indices: 34907--35025 Score: 107
Period size: 43 Copynumber: 3.0 Consensus size: 37
34897 GGGAAAAAGG
*
34907 GAAAAGAAAAAAAAAGAAAGAGGAA-AAAGATA-AAAA
1 GAAAAGAAAAAAAAAGAAAGAGAAAGAAAGA-AGAAAA
*
34943 GAAAAGGGAAAGAAAAAGAAAGAAGAAAGAAAGAAGGAAAA
1 GAAAA--GAAAAAAAAAGAAAG-AGAAAGAAAGAA-GAAAA
34984 GAAAAAGAAAAAGGAAAAGAAAGAAAGAAAGAAAGAAAGAAA
1 G-AAAAGAAAAA--AAAAGAAAG--AGAAAGAAAG-AAGAAA
35026 G
Statistics
Matches: 69, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
36 5 0.07
38 14 0.20
39 5 0.07
40 10 0.14
41 5 0.07
42 13 0.19
43 15 0.22
44 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (37 bp):
GAAAAGAAAAAAAAAGAAAGAGAAAGAAAGAAGAAAA
Found at i:34948 original size:43 final size:43
Alignment explanation
Indices: 34901--35020 Score: 127
Period size: 47 Copynumber: 2.7 Consensus size: 43
34891 AAAATGGGGA
* *
34901 AAAAGGGAAAAGAAAAAAAAAGAAAGAGGAA-AAAGATAAAAAG
1 AAAAGGGAAAAGAAAAAAAAAGAAAGAAGAAGAAA-AGAAAAAG
34944 AAAAGGG-AAAGAAAAAGAAAGAAGAAAGAAAGAAGGAAAAGAAAAAG
1 AAAAGGGAAAAG-AAAA-AAA-AAGAAAG-AAGAA-GAAAAGAAAAAG
*
34991 AAAAAGGAAAAGAAAGAAAGAAAGAAAGAA
1 AAAAGGGAAAAGAAA-AAA-AAAGAAAGAA
35021 AGAAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
42 4 0.06
43 11 0.17
44 3 0.05
45 7 0.11
46 6 0.09
47 25 0.38
48 9 0.14
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (43 bp):
AAAAGGGAAAAGAAAAAAAAAGAAAGAAGAAGAAAAGAAAAAG
Found at i:34960 original size:6 final size:6
Alignment explanation
Indices: 34908--35005 Score: 71
Period size: 6 Copynumber: 16.3 Consensus size: 6
34898 GGAAAAAGGG
* * *
34908 AAAAG- AAAA-A AAAAGA AAGAGGA AAAAGA TAAAA-A GAAAAGG GAAAGA
1 AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA -AAAAGA -AAAAGA AAAAGA
* *
34956 AAAAG- -AAAGA AGAAAGA AAGAAGG AAAAGA AAAAGA AAAAGG AAAAGA
1 AAAAGA AAAAGA A-AAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA
35004 AA
1 AA
35006 GAAAGAAAGA
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 41 0.56
7 20 0.27
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (6 bp):
AAAAGA
Done.