Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019930.1 Corchorus olitorius cultivar O-4 contig19963, 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: 24167
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:521 original size:94 final size:94
Alignment explanation
Indices: 345--521 Score: 225
Period size: 94 Copynumber: 1.9 Consensus size: 94
335 TTTCCTTAAA
*
345 AGGTTAACAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
1 AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
***
410 GAAGATATCACTGTTTCATTCTCATAGGG
66 GAAGATATCAAAATTTCATTCTCATAGGG
* * * *
439 AGGTTATCTAAATTTCAT-GGTGTGGTTATCAAAATTTTAT-GAGGAGGTTATCAAAATTTTATA
1 AGGTTAACAAAATTTCATAGG-GAGGTTATCAAAATTTTATGGA-GAGGTTATCAAAATTATATA
*
502 G-GGAGATTATCAAAATTTCA
64 GAGAAGA-TATCAAAATTTCA
522 CAATGAGGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 8 0.11
94 63 0.89
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (94 bp):
AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
GAAGATATCAAAATTTCATTCTCATAGGG
Found at i:553 original size:22 final size:22
Alignment explanation
Indices: 149--626 Score: 204
Period size: 22 Copynumber: 21.5 Consensus size: 22
139 TTACATGAGA
**
149 AGGTTATCAAAATTTCATACAG
1 AGGTTATCAAAATTTCATAGTG
* ***
171 AGGTTACCAAAATTTCATAAAA
1 AGGTTATCAAAATTTCATAGTG
* *
193 AGGTTATCAAAATTTCTTAGGG
1 AGGTTATCAAAATTTCATAGTG
* * * ***
215 AGATTAACAAAATATCATACAA
1 AGGTTATCAAAATTTCATAGTG
* *
237 AGGTTATCGAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
259 TA-GTTATCAAAATTTAATAAG-A
1 -AGGTTATCAAAATTTCAT-AGTG
* *
281 AGGTTAACAAAATTTCATAGGGAGG
1 AGGTTATCAAAATTTCATA--G-TG
306 AAGGTTATCAAAA-TT--T-GT-
1 -AGGTTATCAAAATTTCATAGTG
* * * **
324 -GCTTATTAAAATTTCCTTA-AA
1 AGGTTATCAAAATTT-CATAGTG
* *
345 AGGTTAACAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * * *
367 AGGTTATGAAAATTTTATGGAG
1 AGGTTATCAAAATTTCATAGTG
*
389 AGGTTATCAAAATTAT-ATAGAG
1 AGGTTATCAAAATT-TCATAGTG
* * ** *
411 AAGATATCACTGTTTCATTCTCATAGGG
1 AGGTTATCA-----AAATT-TCATAGTG
* *
439 AGGTTATCTAAATTTCATGGTG
1 AGGTTATCAAAATTTCATAGTG
* *
461 TGGTTATCAAAATTTTATGAG-G
1 AGGTTATCAAAATTTCAT-AGTG
* *
483 AGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * *
505 AGATTATCAAAATTTCACAATG
1 AGGTTATCAAAATTTCATAGTG
527 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * * **
549 TGGTTATTAAGATTTCACCGTG
1 AGGTTATCAAAATTTCATAGTG
* * * *
571 TGGTTATCAAATTTTCACAGGG
1 AGGTTATCAAAATTTCATAGTG
** * *
593 AGGTTATCGACCATTTCATAATA
1 AGGTTATC-AAAATTTCATAGTG
616 AGGTTATCAAA
1 AGGTTATCAAA
627 TGTTCACAAT
Statistics
Matches: 337, Mismatches: 93, Indels: 52
0.70 0.19 0.11
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
20 2 0.01
21 7 0.02
22 264 0.78
23 25 0.07
25 2 0.01
26 11 0.03
27 4 0.01
28 11 0.03
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:637 original size:22 final size:21
Alignment explanation
Indices: 508--654 Score: 69
Period size: 22 Copynumber: 6.6 Consensus size: 21
498 TATAGGGAGA
*
508 TTATCAAAATTTCACAATGAGG
1 TTATC-AAATTTCACAATAAGG
* * **
530 TTATCAAAATTTCATAGTGTGG
1 TTATC-AAATTTCACAATAAGG
* ** **
552 TTATTAAGATTTCACCGTGTGG
1 TTATCAA-ATTTCACAATAAGG
***
574 TTATCAAATTTTCACAGGGAGG
1 TTATCAAA-TTTCACAATAAGG
* *
596 TTATCGACCATTTCATAATAAGG
1 TTATC-A-AATTTCACAATAAGG
**
619 TTATCAAATGTTCACAATATTG
1 TTATCAAAT-TTCACAATAAGG
641 TTATCAATATTTCA
1 TTATCAA-ATTTCA
655 ACGTTGGAGC
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
21 5 0.05
22 77 0.77
23 17 0.17
24 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (21 bp):
TTATCAAATTTCACAATAAGG
Found at i:1633 original size:47 final size:48
Alignment explanation
Indices: 1537--1633 Score: 160
Period size: 47 Copynumber: 2.0 Consensus size: 48
1527 ATGAATGGTC
* * *
1537 TTAAATTTGTTAATACATATATAAATTTTTTCATAATCGTTATAGCTT
1 TTAAATTTGTTAATACATATATAAACTTTTTCATAATCGTTACAACTT
1585 TTAAATTTGTTAATACATATAT-AACTTTTTCATAATCGTTACAACTT
1 TTAAATTTGTTAATACATATATAAACTTTTTCATAATCGTTACAACTT
1632 TT
1 TT
1634 TCAGTAACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 24 0.52
48 22 0.48
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.49
Consensus pattern (48 bp):
TTAAATTTGTTAATACATATATAAACTTTTTCATAATCGTTACAACTT
Found at i:3548 original size:12 final size:12
Alignment explanation
Indices: 3531--3556 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3521 ACGTACAAAA
3531 TTTTCAATAAAT
1 TTTTCAATAAAT
3543 TTTTCAATAAAT
1 TTTTCAATAAAT
3555 TT
1 TT
3557 GTATGTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTCAATAAAT
Found at i:3627 original size:18 final size:18
Alignment explanation
Indices: 3584--3639 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
3574 GATAATGATG
3584 TGAAAATTTGATAACATCATTA
1 TGAAAATTTGATAAC--C--TA
3606 TG-AAATTTCGATAACCTA
1 TGAAAATTT-GATAACCTA
3624 TGAAAATTTGATAACC
1 TGAAAATTTGATAACC
3640 ATACTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 1 0.03
21 6 0.19
22 8 0.25
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (18 bp):
TGAAAATTTGATAACCTA
Found at i:3650 original size:40 final size:40
Alignment explanation
Indices: 3584--3696 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 40
3574 GATAATGATG
*
3584 TGAAAATTTGATAACATCATTATGAAATTTCGATAACCTA
1 TGAAAATTTGATAACATCACTATGAAATTTCGATAACCTA
* *
3624 TGAAAATTTGATAACCAT-ACTGTGAAATTTTGATAATCTCCCTA
1 TGAAAATTTGATAA-CATCACTATGAAATTTCGATAA----CCTA
* *
3668 TGAAATTTTGATAATCA-CACTATAAAATT
1 TGAAAATTTGATAA-CATCACTATGAAATT
3697 GGTAATCGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
40 29 0.48
41 3 0.05
44 28 0.47
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (40 bp):
TGAAAATTTGATAACATCACTATGAAATTTCGATAACCTA
Found at i:3655 original size:22 final size:22
Alignment explanation
Indices: 3584--4103 Score: 178
Period size: 22 Copynumber: 23.5 Consensus size: 22
3574 GATAATGATG
* * *
3584 TGAAAATTTGATAACATCATTA
1 TGAAATTTTGATAACCTCACTA
*
3606 TGAAATTTCGATAA---C-CTA
1 TGAAATTTTGATAACCTCACTA
* *
3624 TGAAAATTTGATAACCAT-ACTG
1 TGAAATTTTGATAACC-TCACTA
* *
3646 TGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCTCACTA
* *
3668 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCACTA
* * * *
3690 T-AAA-ATTGGTAATCGCACTA
1 TGAAATTTTGATAACCTCACTA
3710 TGAAAATTTTGATAACCCTTCA-TA
1 TG-AAATTTTGATAA-CC-TCACTA
* *
3734 --AAATTTTGATAACCACACCA
1 TGAAATTTTGATAACCTCACTA
* * *
3754 TTAAGTTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCACTA
** * **
3776 TGAGAATGAAACAGTGATATCCTCTTTA
1 TGA-AAT-----TTTGATAACCTCACTA
** * * *
3804 TTTAATTTTGATAACATCTCCA
1 TGAAATTTTGATAACCTCACTA
* *
3826 TAAAATTTTTG-TAACCTTC-CAA
1 TGAAA-TTTTGATAACC-TCACTA
* * *
3848 TAAAATTTTGTTAACCTCCCTA
1 TGAAATTTTGATAACCTCACTA
* * *
3870 GGAAACTTTGATAACCTCCCTCCCTA
1 TGAAATTTTGATAA----CCTCACTA
*
3896 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCACTA
3918 T-AAATTTTGATAACCTTC-CTA
1 TGAAATTTTGATAACC-TCACTA
* * *
3939 T-AAATTTTGTTAACGACACTCTA
1 TGAAATTTTGATAAC--CTCACTA
** * ***
3962 ACAAAATTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTCACTA
* * **
3984 TGAAATTTTGGTAACGTCTGTA
1 TGAAATTTTGATAACCTCACTA
*
4006 TGGAATTTTGATAA-CTACACTA
1 TGAAATTTTGATAACCT-CACTA
**
4028 TGACGTTTTGATAACCTCTA-TA
1 TGAAATTTTGATAACCTC-ACTA
*
4050 TGAAATTTT-AGTAACCACACTA
1 TGAAATTTTGA-TAACCTCACTA
* *
4072 TGAAAATTTGACAACCTTC-CTA
1 TGAAATTTTGATAACC-TCACTA
*
4094 TGTAATTTTG
1 TGAAATTTTG
4104 GTTTGATTGA
Statistics
Matches: 373, Mismatches: 85, Indels: 80
0.69 0.16 0.15
Matches are distributed among these distances:
18 14 0.04
19 3 0.01
20 17 0.05
21 56 0.15
22 208 0.56
23 24 0.06
24 14 0.04
25 2 0.01
26 20 0.05
27 3 0.01
28 12 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCACTA
Found at i:3708 original size:20 final size:21
Alignment explanation
Indices: 3665--3717 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3655 GATAATCTCC
* *
3665 CTATGAAATTTTGATAATCACA
1 CTATGAAA-ATTGGTAATCACA
*
3687 CTAT-AAAATTGGTAATCGCA
1 CTATGAAAATTGGTAATCACA
3707 CTATGAAAATT
1 CTATGAAAATT
3718 TTGATAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.52
21 9 0.33
22 4 0.15
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (21 bp):
CTATGAAAATTGGTAATCACA
Found at i:3717 original size:43 final size:45
Alignment explanation
Indices: 3621--3726 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 45
3611 TTTCGATAAC
* * * * *
3621 CTATGAAAA-TTTGATAACCATACTGTGAAATTTTGATAATCTCC
1 CTATGAAAATTTTGATAACCACACTATGAAATATTGATAATCGCA
* *
3665 CTATG-AAATTTTGATAATCACACTAT-AAA-ATTGGTAATCGCA
1 CTATGAAAATTTTGATAACCACACTATGAAATATTGATAATCGCA
3707 CTATGAAAATTTTGATAACC
1 CTATGAAAATTTTGATAACC
3727 CTTCATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 14 0.27
43 19 0.37
44 19 0.37
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (45 bp):
CTATGAAAATTTTGATAACCACACTATGAAATATTGATAATCGCA
Found at i:3900 original size:26 final size:26
Alignment explanation
Indices: 3862--3911 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3852 ATTTTGTTAA
3862 CCTCCCTAGGAAACTTTGATAACCTC
1 CCTCCCTAGGAAACTTTGATAACCTC
* *
3888 CCTCCCTATGAAATTTTGATAACC
1 CCTCCCTAGGAAACTTTGATAACC
3912 ACACTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (26 bp):
CCTCCCTAGGAAACTTTGATAACCTC
Found at i:5545 original size:120 final size:118
Alignment explanation
Indices: 5269--5618 Score: 612
Period size: 120 Copynumber: 2.9 Consensus size: 118
5259 TGTTAACGTG
*
5269 TTTGGTATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* *
5334 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCG
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCA
*
5387 TTTGGGA-CTTAAGAATTAAGGAGTAATTTATACTATTTTTAATGGAAGAGTTGGTTTGAAGTGG
1 TTTGGGATC-TAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGG
5451 AAAATTTAAGGACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCA
65 AAAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCA
*
5507 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
*
5572 AAATTGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGT
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGT
5619 GGATGTTTTT
Statistics
Matches: 221, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
117 1 0.00
118 108 0.49
120 111 0.50
121 1 0.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (118 bp):
TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTAGAGCA
Found at i:5965 original size:4 final size:4
Alignment explanation
Indices: 5956--5988 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
5946 TAAGATAAGA
5956 TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
5989 CTGTGAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:7668 original size:21 final size:21
Alignment explanation
Indices: 7644--7709 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
7634 AAACACAGTG
7644 AAATCTCATTACAATTCAAAT
1 AAATCTCATTACAATTCAAAT
* * *
7665 AAATCTC--T--AA-CCCAGT
1 AAATCTCATTACAATTCAAAT
7681 GAAATCTCATTACAATTCAAAT
1 -AAATCTCATTACAATTCAAAT
7703 AAATCTC
1 AAATCTC
7710 TATACCCCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
16 3 0.09
17 9 0.27
19 2 0.06
21 16 0.48
22 3 0.09
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.30
Consensus pattern (21 bp):
AAATCTCATTACAATTCAAAT
Found at i:7690 original size:38 final size:39
Alignment explanation
Indices: 7639--7716 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
7629 CAAACAAACA
7639 CAGTGAAATCTCATTACAATTCAAATAAATCTCTA-ACC
1 CAGTGAAATCTCATTACAATTCAAATAAATCTCTATACC
7677 CAGTGAAATCTCATTACAATTCAAATAAATCTCTATACC
1 CAGTGAAATCTCATTACAATTCAAATAAATCTCTATACC
7716 C
1 C
7717 CTCAAACTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 35 0.90
39 4 0.10
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (39 bp):
CAGTGAAATCTCATTACAATTCAAATAAATCTCTATACC
Found at i:7906 original size:121 final size:121
Alignment explanation
Indices: 7692--7935 Score: 461
Period size: 121 Copynumber: 2.0 Consensus size: 121
7682 AAATCTCATT
*
7692 ACAATTCAAATAAATCTCTATACCCCTCAAACTTGCATGTCAAGATCCATTCCCTGCCTTAAATT
1 ACAATTCAAATAAATCTCTATACCCCTCAAACTTGCATGTCAAGATCCATCCCCTGCCTTAAATT
*
7757 CTAATAATACAGAAATGCTAATTTATAAGTCAACAAACCCCTTCCCCAACAAACAA
66 CTAATAATACAGAAATGCTAATTTATAAGTCAACAAAACCCTTCCCCAACAAACAA
7813 ACAATTCAAATAAATCTCTATACCCCTCAAACTTGCATGTCAAGATCCATCCCCTGCCTTAAATT
1 ACAATTCAAATAAATCTCTATACCCCTCAAACTTGCATGTCAAGATCCATCCCCTGCCTTAAATT
*
7878 CTAATAATACAGAAATGCTAATTTATAAGTCAACAAAACCCTTCTCCAACAAACAA
66 CTAATAATACAGAAATGCTAATTTATAAGTCAACAAAACCCTTCCCCAACAAACAA
7934 AC
1 AC
7936 CCAGTGAAAT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.26
Consensus pattern (121 bp):
ACAATTCAAATAAATCTCTATACCCCTCAAACTTGCATGTCAAGATCCATCCCCTGCCTTAAATT
CTAATAATACAGAAATGCTAATTTATAAGTCAACAAAACCCTTCCCCAACAAACAA
Done.