Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022235.1 Corchorus olitorius cultivar O-4 contig22268, 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: 44923
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2473 original size:26 final size:27
Alignment explanation
Indices: 2418--2488 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 27
2408 GATCACCTAG
*
2418 GGGGCATTCTGGTCATTTTCACACTAA
1 GGGGCATTCTGGTCATTTGCACACTAA
* * * *
2445 -GGGCATCCTGGTCATTTGCATATTCA
1 GGGGCATTCTGGTCATTTGCACACTAA
*
2471 GGGGCATTTTGGTCATTT
1 GGGGCATTCTGGTCATTT
2489 TCGGTCCACT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (27 bp):
GGGGCATTCTGGTCATTTGCACACTAA
Found at i:2942 original size:28 final size:28
Alignment explanation
Indices: 2907--2964 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2897 TGTATTACAT
2907 ATTTTCTTAATTTCATGCATAGCATTAC
1 ATTTTCTTAATTTCATGCATAGCATTAC
2935 ATTTTCTTAATTTCATGCATAGCATTAC
1 ATTTTCTTAATTTCATGCATAGCATTAC
2963 AT
1 AT
2965 CATTTTGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (28 bp):
ATTTTCTTAATTTCATGCATAGCATTAC
Found at i:9128 original size:2 final size:2
Alignment explanation
Indices: 9121--9186 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
9111 TCCTGATCCC
9121 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9162 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
9187 GTTCTATTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:11067 original size:34 final size:34
Alignment explanation
Indices: 11022--11092 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
11012 AGTTTCTTTC
11022 TTTTACCTGTTTCAAAATTCCATATTAAGCACTA
1 TTTTACCTGTTTCAAAATTCCATATTAAGCACTA
* * * *
11056 TTTTACTTGTTTTAAAATTCCGTATTTAGCACTA
1 TTTTACCTGTTTCAAAATTCCATATTAAGCACTA
11090 TTT
1 TTT
11093 AATAGTGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (34 bp):
TTTTACCTGTTTCAAAATTCCATATTAAGCACTA
Found at i:12882 original size:23 final size:23
Alignment explanation
Indices: 12854--12898 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
12844 TTTCCTTGGT
12854 TAATTTTAATTACTAACAAGTCA
1 TAATTTTAATTACTAACAAGTCA
12877 TAATTTTAATTACTAACAAGTC
1 TAATTTTAATTACTAACAAGTC
12899 CTTGTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (23 bp):
TAATTTTAATTACTAACAAGTCA
Found at i:16812 original size:15 final size:15
Alignment explanation
Indices: 16794--16823 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16784 TATATTTGCC
16794 ATATATATAGATAAT
1 ATATATATAGATAAT
*
16809 ATATATTTAGATAAT
1 ATATATATAGATAAT
16824 CTGTTGCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
ATATATATAGATAAT
Found at i:24935 original size:19 final size:19
Alignment explanation
Indices: 24911--24947 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24901 TTACAGTACC
24911 TAATCTAATCTATACAGTG
1 TAATCTAATCTATACAGTG
* *
24930 TAATCTCATCTGTACAGT
1 TAATCTAATCTATACAGT
24948 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTATACAGTG
Found at i:27026 original size:13 final size:14
Alignment explanation
Indices: 27008--27048 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
26998 TTTGACCTTT
27008 AATTATAAAAAA-A
1 AATTATAAAAAATA
27021 AATTATATAAAAATA
1 AATTATA-AAAAATA
*
27036 AATTTTAAAAAAT
1 AATTATAAAAAAT
27049 TATGTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 7 0.28
14 11 0.44
15 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTATAAAAAATA
Found at i:27031 original size:15 final size:14
Alignment explanation
Indices: 27010--27047 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
27000 TGACCTTTAA
27010 TTATAAAAAAAAAT
1 TTATAAAAAAAAAT
*
27024 TATATAAAAATAAAT
1 T-TATAAAAAAAAAT
27039 TT-TAAAAAA
1 TTATAAAAAA
27048 TTATGTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 6 0.29
14 2 0.10
15 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TTATAAAAAAAAAT
Found at i:40288 original size:13 final size:13
Alignment explanation
Indices: 40270--40294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40260 GTTATCAAAT
40270 TTACAGTAATTAG
1 TTACAGTAATTAG
40283 TTACAGTAATTA
1 TTACAGTAATTA
40295 TCAAATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAG
Found at i:42096 original size:22 final size:21
Alignment explanation
Indices: 42065--42259 Score: 100
Period size: 22 Copynumber: 9.1 Consensus size: 21
42055 GATAATGATG
* * *
42065 TGAAAATTTGATAACATCATTA
1 TGAAATTTTGATAAC-CCACTA
42087 TGAAATTTTG-TAA--C-CTA
1 TGAAATTTTGATAACCCACTA
* *
42104 TGAAAATTTGATAACCACACTG
1 TGAAATTTTGATAACC-CACTA
42126 TGAAATTTTGATAATCTCC-CTA
1 TGAAATTTTGATAA-C-CCACTA
*
42148 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAA-CCCACTA
* *
42170 T-AAAATTAG-TAACCGCACTA
1 TGAAATTTTGATAACC-CACTA
*
42190 TGAAAATTTTGATAACCTC-TTCA
1 TG-AAATTTTGATAACC-CACT-A
* * *
42213 TAAAATTTTAATAACCACACCA
1 TGAAATTTTGATAACC-CACTA
* * *
42235 TTAAGTTTTGATAACCTCCCTA
1 TGAAATTTTGATAACC-CACTA
42257 TGA
1 TGA
42260 GAATGAAACA
Statistics
Matches: 133, Mismatches: 26, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
17 11 0.08
18 4 0.03
19 1 0.01
20 9 0.07
21 11 0.08
22 86 0.65
23 10 0.08
24 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (21 bp):
TGAAATTTTGATAACCCACTA
Found at i:42118 original size:18 final size:19
Alignment explanation
Indices: 42050--42120 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 19
42040 ATGTCATTTG
** *
42050 AATTTGATAATGATGTGAA
1 AATTTGATAACCATATGAA
42069 AATTTGATAACATCATTATGAA
1 AATTTGATAAC--CA-TATGAA
*
42091 ATTTTG-TAACC-TATGAA
1 AATTTGATAACCATATGAA
42108 AATTTGATAACCA
1 AATTTGATAACCA
42121 CACTGTGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 11 0.26
18 5 0.12
19 11 0.26
21 5 0.12
22 10 0.24
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (19 bp):
AATTTGATAACCATATGAA
Found at i:42197 original size:43 final size:45
Alignment explanation
Indices: 42101--42206 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 45
42091 ATTTTGTAAC
* * * * * *
42101 CTATGAAAA-TTTGATAACCACACTGTGAAATTTTGATAATCTCC
1 CTATGAAAATTTTGATAACCACACTATGAAAATTAGATAACCGCA
*
42145 CTATG-AAATTTTGATAATCACACTAT-AAAATTAG-TAACCGCA
1 CTATGAAAATTTTGATAACCACACTATGAAAATTAGATAACCGCA
42187 CTATGAAAATTTTGATAACC
1 CTATGAAAATTTTGATAACC
42207 TCTTCATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 10 0.19
43 22 0.42
44 20 0.38
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (45 bp):
CTATGAAAATTTTGATAACCACACTATGAAAATTAGATAACCGCA
Found at i:42219 original size:65 final size:66
Alignment explanation
Indices: 42101--42232 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 66
42091 ATTTTGTAAC
* * * * * *
42101 CTATGAAAATTTGATAACCACACTGTGAAATTTTGATAATCTCCCTATGAAATTTTGATAATCAC
1 CTATGAAAATTAGATAACCACACTATGAAATTTTGATAACCTCCCTATAAAATTTTAATAACCAC
42166 A
66 A
* *
42167 CTAT-AAAATTAG-TAACCGCACTATGAAAATTTTGATAACCT-CTTCATAAAATTTTAATAACC
1 CTATGAAAATTAGATAACCACACTATG-AAATTTTGATAACCTCCCT-ATAAAATTTTAATAACC
42229 ACA
64 ACA
42232 C
1 C
42233 CATTAAGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
64 13 0.23
65 39 0.70
66 4 0.07
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (66 bp):
CTATGAAAATTAGATAACCACACTATGAAATTTTGATAACCTCCCTATAAAATTTTAATAACCAC
A
Found at i:42355 original size:22 final size:22
Alignment explanation
Indices: 42330--42371 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42320 ACCTTCCAAT
* * *
42330 GAAATTTTGTTAATCTCCCTAG
1 GAAACTTTGATAACCTCCCTAG
42352 GAAACTTTGATAACCTCCCT
1 GAAACTTTGATAACCTCCCT
42372 CCCTATGAAA
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:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (22 bp):
GAAACTTTGATAACCTCCCTAG
Found at i:42381 original size:26 final size:26
Alignment explanation
Indices: 42344--42393 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
42334 TTTTGTTAAT
42344 CTCCCTAGGAAACTTTGATAACCTCC
1 CTCCCTAGGAAACTTTGATAACCTCC
* *
42370 CTCCCTATGAAATTTTGATAACCT
1 CTCCCTAGGAAACTTTGATAACCT
42394 TCGTATAAAA
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:0.30, G:0.10, T:0.32
Consensus pattern (26 bp):
CTCCCTAGGAAACTTTGATAACCTCC
Found at i:42454 original size:22 final size:22
Alignment explanation
Indices: 42375--42519 Score: 96
Period size: 22 Copynumber: 6.5 Consensus size: 22
42365 CCTCCCTCCC
42375 TATGAAATTTTGATAACCT-TCG
1 TATGAAATTTTGATAACCTCT-G
* * * *
42397 TATAAAATTTTGTTAACGACACTC
1 TATGAAATTTTGATAAC--CTCTG
* * * *
42421 TAAGAAAATTTGATAACCTTTT
1 TATGAAATTTTGATAACCTCTG
* *
42443 TATGAAATTTTGGTAACGTCTG
1 TATGAAATTTTGATAACCTCTG
* **
42465 TATGGAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCT-CTG
** *
42487 TATGACGTTTTGATAACCTCTA
1 TATGAAATTTTGATAACCTCTG
42509 TATGAAATTTT
1 TATGAAATTTT
42520 TGTAACCACA
Statistics
Matches: 89, Mismatches: 29, Indels: 10
0.70 0.23 0.08
Matches are distributed among these distances:
21 1 0.01
22 71 0.80
23 2 0.02
24 14 0.16
25 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTG
Found at i:42491 original size:44 final size:44
Alignment explanation
Indices: 42443--42549 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
42433 ATAACCTTTT
* * * * *
42443 TATGAAATTTTGGTAACGTCTGTATGGAA-TTTTGATAACTACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTTG-TAACCACAC
**
42487 TATGACGTTTTGATAACCTCTATATGAAATTTTTGTAACCACAC
1 TATGAAATTTTGATAACCTCTATATGAAATTTTTGTAACCACAC
* *
42531 TATGAAAATTTGACAACCT
1 TATGAAATTTTGATAACCT
42550 TCCTATGTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 46 0.90
45 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCTATATGAAATTTTTGTAACCACAC
Found at i:43608 original size:40 final size:40
Alignment explanation
Indices: 43553--43629 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
43543 AACTTGGACA
43553 GAATCAAAGACTTATCATCAATTAATCATAGTAAATAATT
1 GAATCAAAGACTTATCATCAATTAATCATAGTAAATAATT
*
43593 GAATCAAATACTTATCATCAATTAATCATAGTAAATA
1 GAATCAAAGACTTATCATCAATTAATCATAGTAAATA
43630 TTTGTATTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (40 bp):
GAATCAAAGACTTATCATCAATTAATCATAGTAAATAATT
Found at i:43619 original size:22 final size:22
Alignment explanation
Indices: 43554--43620 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
43544 ACTTGGACAG
*
43554 AATCAAAGACTTATCATCAATT
1 AATCAAATACTTATCATCAATT
* *
43576 AATC--ATA-GTA-AAT-AATT
1 AATCAAATACTTATCATCAATT
43593 GAATCAAATACTTATCATCAATT
1 -AATCAAATACTTATCATCAATT
43616 AATCA
1 AATCA
43621 TAGTAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
17 4 0.12
18 6 0.18
19 2 0.06
20 5 0.15
21 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (22 bp):
AATCAAATACTTATCATCAATT
Done.