Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012088.1 Corchorus olitorius cultivar O-4 contig12121, 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: 63711
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:8275 original size:8 final size:8
Alignment explanation
Indices: 8262--8299 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
8252 AACTAAAAAT
8262 AATATATA
1 AATATATA
8270 AATATATA
1 AATATATA
8278 AATATATA
1 AATATATA
8286 AATATATA
1 AATATATA
*
8294 TATATA
1 AATATA
8300 ATACCAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATATA
Found at i:8906 original size:18 final size:19
Alignment explanation
Indices: 8883--8920 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
8873 TACGAATTGG
8883 CGTCAAATAGGGGCA-ATC
1 CGTCAAATAGGGGCAGATC
* *
8901 CGTCAATTTGGGGCAGATC
1 CGTCAAATAGGGGCAGATC
8920 C
1 C
8921 TTTTCGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (19 bp):
CGTCAAATAGGGGCAGATC
Found at i:9447 original size:86 final size:83
Alignment explanation
Indices: 9348--9518 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 83
9338 TTTCCAGAAA
* * *
9348 TATCGAAAAACCCATAAACAATTCAACCCAAAAAATCATAAAACAACATTTTTTTTTCTAGAAAC
1 TATCGAAAAACCCATAAACAATTCAACCCAAAAAATCATAAAACAACA---ATTTTTCCAAAAAC
*
9413 CCATAACCCAGAATCAATTAT
63 CCATAACCCAAAATCAATTAT
*
9434 TATCGAAAAACCCATAAACAATTTAACCCAAAAAATCATAAAACAACAATTTTTCCAAAAACCCA
1 TATCGAAAAACCCATAAACAATTCAACCCAAAAAATCATAAAACAACAATTTTTCCAAAAACCCA
*
9499 TAACCCAAAATCGATTAT
66 TAACCCAAAATCAATTAT
9517 TA
1 TA
9519 CCCAAAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
83 32 0.41
86 47 0.59
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.24
Consensus pattern (83 bp):
TATCGAAAAACCCATAAACAATTCAACCCAAAAAATCATAAAACAACAATTTTTCCAAAAACCCA
TAACCCAAAATCAATTAT
Found at i:9536 original size:86 final size:84
Alignment explanation
Indices: 9360--9537 Score: 214
Period size: 86 Copynumber: 2.1 Consensus size: 84
9350 TCGAAAAACC
* * * *
9360 CATAAACAATTCAACCCAAAAAATCATAAAACAACATTTTTTTTTCTAGAAACCCATAACCCAGA
1 CATAAACAATTCAACCCAAAAAATCATAAAACAACA--TATTTTTCCAAAAACCCATAACCCAAA
* * **
9425 ATCAATTATTATCGAAAAACC
64 ATCAATTATTACCAAAAAAAA
*
9446 CATAAACAATTTAACCCAAAAAATCATAAAACAACA-ATTTTTCCAAAAACCCATAACCCAAAAT
1 CATAAACAATTCAACCCAAAAAATCATAAAACAACATATTTTTCCAAAAACCCATAACCCAAAAT
*
9510 CGATTATTACCCAAAAAATGAA
66 CAATTATTA-CCAAAAAA--AA
9532 CATAAA
1 CATAAA
9538 AACACAAGCA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 32 0.41
84 6 0.08
86 41 0.52
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (84 bp):
CATAAACAATTCAACCCAAAAAATCATAAAACAACATATTTTTCCAAAAACCCATAACCCAAAAT
CAATTATTACCAAAAAAAA
Found at i:11171 original size:2 final size:2
Alignment explanation
Indices: 11158--11212 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
11148 AGAAAACAAA
* *
11158 AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
11200 AG AG AG GG AG AG A
1 AG AG AG AG AG AG A
11213 AGGAAAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.04, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11431 original size:20 final size:20
Alignment explanation
Indices: 11408--11450 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
11398 TTTGTTCAAT
11408 TTTCTTTTGATGTTTGTAAG
1 TTTCTTTTGATGTTTGTAAG
11428 TTTCTTTTGATGTTTGTAAG
1 TTTCTTTTGATGTTTGTAAG
11448 TTT
1 TTT
11451 GGCATATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.63
Consensus pattern (20 bp):
TTTCTTTTGATGTTTGTAAG
Found at i:12228 original size:2 final size:2
Alignment explanation
Indices: 12221--12270 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
12211 TTTTAGGGCT
12221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
12263 TG TA TA TA
1 TA TA TA TA
12271 ATTGACGTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17075 original size:2 final size:2
Alignment explanation
Indices: 17068--17110 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
17058 TGCGATGATC
17068 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
17110 A
1 A
17111 CTCATGCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21219 original size:28 final size:28
Alignment explanation
Indices: 21179--21243 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
21169 AAGTAAAAAT
21179 GAGAATTAAATTGAGAGTAAAACCACAA
1 GAGAATTAAATTGAGAGTAAAACCACAA
**
21207 GAGAATTAAATTGAGAGTAAAATTACAA
1 GAGAATTAAATTGAGAGTAAAACCACAA
21235 GAGAATTAA
1 GAGAATTAA
21244 GATGGAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (28 bp):
GAGAATTAAATTGAGAGTAAAACCACAA
Found at i:26091 original size:2 final size:2
Alignment explanation
Indices: 26084--26113 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26074 TTTCTTGTTT
26084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26114 ATTCATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26749 original size:20 final size:18
Alignment explanation
Indices: 26710--26759 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
26700 TGTTCATCGG
26710 ATATATATATAGTCTGAT
1 ATATATATATAGTCTGAT
26728 ATATACTATATTAGTCAT-AT
1 ATATA-TATA-TAGTC-TGAT
26748 ATATTATATATA
1 ATA-TATATATA
26760 TTCTATAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 5 0.18
19 6 0.21
20 14 0.50
21 3 0.11
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATATATATAGTCTGAT
Found at i:27019 original size:1 final size:1
Alignment explanation
Indices: 27013--27044 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
27003 AGCTTGGTTC
27013 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27045 CGATTGAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28485 original size:36 final size:36
Alignment explanation
Indices: 28442--28511 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
28432 CTGTCACAAC
*
28442 TTTGTACTCCACTCTTGTCTGGCATAAGGAGAAACT
1 TTTGTACTCCACTCTTGTCTGACATAAGGAGAAACT
* *
28478 TTTGTACTCCATTCTTGTCTGATATAAGGAGAAA
1 TTTGTACTCCACTCTTGTCTGACATAAGGAGAAA
28512 ATTAACTAAC
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:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (36 bp):
TTTGTACTCCACTCTTGTCTGACATAAGGAGAAACT
Found at i:30594 original size:30 final size:30
Alignment explanation
Indices: 30558--30614 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
30548 CATTGGAAAA
30558 TTCTCTGCCATAGTCTCCAGCAGAGCAATG
1 TTCTCTGCCATAGTCTCCAGCAGAGCAATG
* *
30588 TTCTCTGTCGTAGTCTCCAGCAGAGCA
1 TTCTCTGCCATAGTCTCCAGCAGAGCA
30615 CCGTCTCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (30 bp):
TTCTCTGCCATAGTCTCCAGCAGAGCAATG
Found at i:30759 original size:24 final size:24
Alignment explanation
Indices: 30723--30769 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
30713 ATTGTTTAAC
** *
30723 TAATTAGTTTCAATTTTAATTATG
1 TAATTAGGATCAATTGTAATTATG
30747 TAATTAGGATCAATTGTAATTAT
1 TAATTAGGATCAATTGTAATTAT
30770 AGCTAACCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
TAATTAGGATCAATTGTAATTATG
Found at i:33920 original size:7 final size:7
Alignment explanation
Indices: 33908--33939 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
33898 AAATAATATT
33908 TATAGTA
1 TATAGTA
33915 TATAGTA
1 TATAGTA
33922 TATAGTA
1 TATAGTA
33929 TATAGTA
1 TATAGTA
33936 TATA
1 TATA
33940 TGTGGTATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TATAGTA
Found at i:52013 original size:21 final size:21
Alignment explanation
Indices: 51961--52014 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
51951 TGGATTGGAG
* *
51961 TATTTA-TTTATCTTGTTGCT
1 TATTTATTTTATTTTCTTGCT
*
51981 TAATTT-TATTATTTTCTTGCT
1 T-ATTTATTTTATTTTCTTGCT
52002 TATTTATTTTATT
1 TATTTATTTTATT
52015 GTTACTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTTATTTTATTTTCTTGCT
Found at i:58366 original size:28 final size:28
Alignment explanation
Indices: 58329--58383 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
58319 TATTGCGTCA
* *
58329 ATGACGTTTTGCCCATGAACTT-CAAATC
1 ATGACATTTTACCCAT-AACTTCCAAATC
*
58357 ATGACATTTTACCCCTAACTTCCAAAT
1 ATGACATTTTACCCATAACTTCCAAAT
58384 TTAGGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (28 bp):
ATGACATTTTACCCATAACTTCCAAATC
Found at i:60614 original size:15 final size:16
Alignment explanation
Indices: 60594--60631 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
60584 CGTTCAAATG
60594 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
60609 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
60626 T-GGGTC
1 TCGGGTC
60632 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:62198 original size:16 final size:17
Alignment explanation
Indices: 62171--62246 Score: 79
Period size: 16 Copynumber: 4.7 Consensus size: 17
62161 GTCGGGTTGA
62171 TCGGGTTCGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
62188 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
* *
62204 TCGGGTTCAGGTC-GTT
1 TCGGGTTCGGGTCATTT
* *
62220 T-GGATTCGGGT-AATT
1 TCGGGTTCGGGTCATTT
62235 TCGGGTTCGGGT
1 TCGGGTTCGGGT
62247 ACCCAAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
15 11 0.23
16 27 0.56
17 10 0.21
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:63591 original size:31 final size:31
Alignment explanation
Indices: 63556--63618 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
63546 TTTAGCTTTC
63556 ACCCTTGGTTAGAATAGAGATCCGACCATTA
1 ACCCTTGGTTAGAATAGAGATCCGACCATTA
*
63587 ACCCTTGGTTAGAATAGAGATTCGACCATTA
1 ACCCTTGGTTAGAATAGAGATCCGACCATTA
63618 A
1 A
63619 TACTTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
ACCCTTGGTTAGAATAGAGATCCGACCATTA
Done.