Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015920.1 Corchorus olitorius cultivar O-4 contig15953, 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: 52228
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:363 original size:29 final size:29
Alignment explanation
Indices: 317--435 Score: 213
Period size: 29 Copynumber: 4.1 Consensus size: 29
307 AAAACACCTT
*
317 GATGTGC-AAAATGACCAAAATGCCCCTG
1 GATGTGCAAAAATGACCAAAATGCCACTG
*
345 GATGTGCAAAAATGACCAAAATGCCCCTG
1 GATGTGCAAAAATGACCAAAATGCCACTG
374 GATGTGCAAAAATGACCAAAATGCCACTG
1 GATGTGCAAAAATGACCAAAATGCCACTG
403 GATGTGCAAAAATGACCAAAATGCCACTG
1 GATGTGCAAAAATGACCAAAATGCCACTG
432 GATG
1 GATG
436 AGCGACCCTA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
28 7 0.08
29 82 0.92
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (29 bp):
GATGTGCAAAAATGACCAAAATGCCACTG
Found at i:1832 original size:30 final size:30
Alignment explanation
Indices: 1775--1848 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1765 GGCAACGACA
* *
1775 TTGTTCAGAAAAAAAAAAATAAACCAATCAT
1 TTGTGCAG-AAAAAAAAAACAAACCAATCAT
* * * *
1806 TTGTGCTGAAAAAAAAAACCAGCCAATCTT
1 TTGTGCAGAAAAAAAAAACAAACCAATCAT
*
1836 TTGTTCAGAAAAA
1 TTGTGCAGAAAAA
1849 GCTCTTTTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 29 0.83
31 6 0.17
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (30 bp):
TTGTGCAGAAAAAAAAAACAAACCAATCAT
Found at i:2915 original size:1 final size:1
Alignment explanation
Indices: 2909--2946 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
2899 CATTGTTCAG
2909 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2947 CAAACAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4063 original size:22 final size:22
Alignment explanation
Indices: 4016--4096 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 22
4006 TTAAATTTGT
*
4016 ATAAAATATATT-TTTA-TAATA
1 ATAAAAT-TATTATATATTAATA
*
4037 TTAAAATTATTATATATTAATA
1 ATAAAATTATTATATATTAATA
*
4059 AT-AAATT-TTCT-T-TTAATA
1 ATAAAATTATTATATATTAATA
4077 TTATATAAATTATTATATAT
1 --ATA-AAATTATTATATAT
4097 ATGATAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
18 6 0.13
19 1 0.02
20 9 0.20
21 14 0.30
22 11 0.24
23 3 0.07
24 1 0.02
25 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAAATTATTATATATTAATA
Found at i:4108 original size:15 final size:14
Alignment explanation
Indices: 4078--4118 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
4068 CTTTTAATAT
* *
4078 TATATAAATTATTA
1 TATATATATAATTA
4092 TATATATGATAATTA
1 TATATAT-ATAATTA
4107 TATATATATAAT
1 TATATATATAAT
4119 AATGATGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TATATATATAATTA
Found at i:4110 original size:17 final size:18
Alignment explanation
Indices: 4084--4121 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
4074 ATATTATATA
*
4084 AATTATTATATATATGAT
1 AATTATTATATATATAAT
4102 AATTA-TATATATATAAT
1 AATTATTATATATATAAT
4119 AAT
1 AAT
4122 GATGATGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTATTATATATATAAT
Found at i:6098 original size:40 final size:40
Alignment explanation
Indices: 6053--6131 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
6043 CATTGGTAAT
6053 ATTTAATCATCAATCATCATCACTGCAAATCTACCAAGAC
1 ATTTAATCATCAATCATCATCACTGCAAATCTACCAAGAC
6093 ATTTAATCATCAATCATCATCACTGCAAATCTACCAAGA
1 ATTTAATCATCAATCATCATCACTGCAAATCTACCAAGA
6132 AATCTTTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.28
Consensus pattern (40 bp):
ATTTAATCATCAATCATCATCACTGCAAATCTACCAAGAC
Found at i:13778 original size:16 final size:16
Alignment explanation
Indices: 13757--13816 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
13747 TGTGGCTTTG
13757 TAAGTGAGTATCT-CAC
1 TAAGTGAGTAT-TACAC
13773 TAAGTGAGTATTACAC
1 TAAGTGAGTATTACAC
*
13789 CAAGTGAGTATGGTAC-C
1 TAAGTGAGTAT--TACAC
13806 -AAGTGAGTATT
1 TAAGTGAGTATT
13817 TTGTTGGGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 1 0.03
15 1 0.03
16 34 0.85
17 1 0.03
18 3 0.08
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (16 bp):
TAAGTGAGTATTACAC
Found at i:16599 original size:16 final size:17
Alignment explanation
Indices: 16578--16614 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
16568 GATATTCTCT
*
16578 TTTTG-ATTTTTTTGGG
1 TTTTGAATTTTTTTGGA
16594 TTTTGAATTTTTTTGGA
1 TTTTGAATTTTTTTGGA
16611 TTTT
1 TTTT
16615 TTTAAACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.11, C:0.00, G:0.19, T:0.70
Consensus pattern (17 bp):
TTTTGAATTTTTTTGGA
Found at i:17616 original size:14 final size:13
Alignment explanation
Indices: 17597--17648 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
17587 TCGTTTGGCA
17597 TTGTTTTCGTTTTT
1 TTGTTTT-GTTTTT
*
17611 TTGTTTTTTTGTTT
1 TTGTTTTGTT-TTT
17625 TTGTTTTG--TTT
1 TTGTTTTGTTTTT
*
17636 TCGTTTTGTTTTT
1 TTGTTTTGTTTTT
17649 GTTGCGCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 10 0.31
13 5 0.16
14 17 0.53
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (13 bp):
TTGTTTTGTTTTT
Found at i:17631 original size:11 final size:11
Alignment explanation
Indices: 17597--17651 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
17587 TCGTTTGGCA
*
17597 TTGTTTTCGTT
1 TTGTTTTTGTT
*
17608 TT-TTTGTTTTT
1 TTGTTT-TTGTT
17619 TTGTTTTTGTT
1 TTGTTTTTGTT
*
17630 TTGTTTTCGTT
1 TTGTTTTTGTT
17641 TTGTTTTTGTT
1 TTGTTTTTGTT
17652 GCGCTGTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 3 0.08
11 31 0.84
12 3 0.08
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (11 bp):
TTGTTTTTGTT
Found at i:20672 original size:30 final size:30
Alignment explanation
Indices: 20588--20691 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
20578 ATGCAATCAT
* * *
20588 TTTGACAAAAGAAATTTGCCTATAATCCTC
1 TTTGAAAAAAGAAATTTGCATATGATCCTC
* *
20618 TTTGAAAAAATAAATTTGCATATGATCTTC
1 TTTGAAAAAAGAAATTTGCATATGATCCTC
* **
20648 TTTGAAAAAAGAAATTTGCTTATGAGGCTC
1 TTTGAAAAAAGAAATTTGCATATGATCCTC
*
20678 TTAGAAAAAA-AAAT
1 TTTGAAAAAAGAAAT
20692 AAATAAATTG
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 4 0.06
30 59 0.94
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (30 bp):
TTTGAAAAAAGAAATTTGCATATGATCCTC
Found at i:31053 original size:3 final size:3
Alignment explanation
Indices: 31045--31073 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31035 GACAATACTA
31045 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
31074 AGCTGCTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31988 original size:8 final size:8
Alignment explanation
Indices: 31975--32003 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
31965 AATTAATAGT
31975 AATAATTA
1 AATAATTA
31983 AATAATT-
1 AATAATTA
31990 AATAATTA
1 AATAATTA
31998 AATAAT
1 AATAAT
32004 AGTAACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATAATTA
Found at i:31994 original size:15 final size:15
Alignment explanation
Indices: 31974--32003 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31964 AAATTAATAG
31974 TAATAATTAAATAAT
1 TAATAATTAAATAAT
31989 TAATAATTAAATAAT
1 TAATAATTAAATAAT
32004 AGTAACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAATTAAATAAT
Found at i:34309 original size:17 final size:17
Alignment explanation
Indices: 34273--34309 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34263 GGGACAATAT
*
34273 ATTTTTGAAATGCCTTG
1 ATTTTTGAAATGCCTCG
*
34290 ATTTTTGAAATGGCTCG
1 ATTTTTGAAATGCCTCG
34307 ATT
1 ATT
34310 AGAAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (17 bp):
ATTTTTGAAATGCCTCG
Found at i:36501 original size:28 final size:30
Alignment explanation
Indices: 36469--36526 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
36459 TTGCTCCGTG
36469 CAAAAT-CTCAAGC-CCTGTGC-TTTTCTCT
1 CAAAATGCTCAAGCTCC-GTGCTTTTTCTCT
*
36497 CAAAATGTTCAAGCTCCGTGCTTTTTCTCT
1 CAAAATGCTCAAGCTCCGTGCTTTTTCTCT
36527 ATAGCTCCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 10 0.38
30 10 0.38
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (30 bp):
CAAAATGCTCAAGCTCCGTGCTTTTTCTCT
Found at i:36546 original size:21 final size:21
Alignment explanation
Indices: 36508--36547 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36498 AAAATGTTCA
* * *
36508 AGCTCCGTGCTTTTTCTCTAT
1 AGCTCCGCGCTATGTCTCTAT
36529 AGCTCCGCGCTATGTCTCT
1 AGCTCCGCGCTATGTCTCT
36548 CTCTCTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.33, G:0.17, T:0.40
Consensus pattern (21 bp):
AGCTCCGCGCTATGTCTCTAT
Found at i:37081 original size:2 final size:2
Alignment explanation
Indices: 37074--37108 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
37064 GTACTTACGA
*
37074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37109 CTATGTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37386 original size:39 final size:38
Alignment explanation
Indices: 37337--37411 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 38
37327 TCCTATGTAA
37337 TAATATATAATAACTAAAATACTTACATTAATTAAACG
1 TAATATATAATAACTAAAATACTTACATTAATTAAACG
*
37375 TAATACTATAATAACTGAAATACTTACATTAATTAAA
1 TAATA-TATAATAACTAAAATACTTACATTAATTAAA
37412 TTTTTAGGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.35
Consensus pattern (38 bp):
TAATATATAATAACTAAAATACTTACATTAATTAAACG
Found at i:37766 original size:204 final size:202
Alignment explanation
Indices: 37524--37934 Score: 743
Period size: 204 Copynumber: 2.0 Consensus size: 202
37514 TTCCTTAATA
37524 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
37589 ATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGT
66 ATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAAT
* *
37654 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAA-TTAATAATAT
129 AATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTTAATAACAT
37718 TCACCATTG
194 TCACCATTG
37727 ATAAATAAATCGGATCCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGAT-CTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
37792 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATA
65 AATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAATA
37857 ATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTTAATAACATT
130 ATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTTAATAACATT
37922 CACCATTG
195 CACCATTG
37930 ATAAA
1 ATAAA
37935 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
202 65 0.32
203 39 0.19
204 97 0.48
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAATAA
TGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTTAATAACATTC
ACCATTG
Found at i:38496 original size:36 final size:36
Alignment explanation
Indices: 38449--38518 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
38439 GAGATTTTGG
* *
38449 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAAACAAAATCACAAAAAATGTAATA
*
38485 AGAAATATGATAAACAAAATCACAAAAGATGTAA
1 AGAAATATGATAAACAAAATCACAAAAAATGTAA
38519 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:0.61, C:0.07, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAAACAAAATCACAAAAAATGTAATA
Found at i:43134 original size:7 final size:7
Alignment explanation
Indices: 43122--43168 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
43112 CTCTGCTCTG
43122 CTTTGAA
1 CTTTGAA
43129 CTTTGAA
1 CTTTGAA
43136 CTTTGAA
1 CTTTGAA
43143 CTTTGAA
1 CTTTGAA
43150 CTTTGAA
1 CTTTGAA
43157 CTTTGAA
1 CTTTGAA
43164 CTTTG
1 CTTTG
43169 CTTGCGATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (7 bp):
CTTTGAA
Done.