Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013015.1 Corchorus olitorius cultivar O-4 contig13048, 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: 59982
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:515 original size:21 final size:21
Alignment explanation
Indices: 476--524 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
466 TCAATGCTTT
**
476 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
498 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
519 A-GAAGC
1 AGGAAGC
525 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:10414 original size:173 final size:173
Alignment explanation
Indices: 10125--10442 Score: 627
Period size: 173 Copynumber: 1.8 Consensus size: 173
10115 CATTTCCTAA
10125 GGACCTCTCACACCAAGATCGATGTTTTTGATGGTTCATTGACAATGGAGTTTGATGGTGATGTT
1 GGACCTCTCACACCAAGATCGATGTTTTTGATGGTTCATTGACAATGGAGTTTGATGGTGATGTT
10190 ATTCATCCTAAAATTTCATCTAATTTATCTTTGAAAACTAATGATTTTGTTTGTGTAGTGGAAAA
66 ATTCATCCTAAAATTTCATCTAATTTATCTTTGAAAACTAATGATTTTGTTTGTGTAGTGGAAAA
10255 GTGGGTAAAGAAAGATCGATGTTTTTGATGGTTCATTGACAAT
131 GTGGGTAAAGAAAGATCGATGTTTTTGATGGTTCATTGACAAT
10298 GGACCTCTCACACCAAGATCGATGTTTTTGATGGTTCATTGACAATGGAGTTTGATGGTGATGTT
1 GGACCTCTCACACCAAGATCGATGTTTTTGATGGTTCATTGACAATGGAGTTTGATGGTGATGTT
*
10363 ATTCATCCTAAAATTTCATCTAATTTATGTTTGAAAACTAATGATTTTGTTTGTGTAGTGGAAAA
66 ATTCATCCTAAAATTTCATCTAATTTATCTTTGAAAACTAATGATTTTGTTTGTGTAGTGGAAAA
10428 GTGGGTAAAGAAAGA
131 GTGGGTAAAGAAAGA
10443 GTTAGGTGAA
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 144 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (173 bp):
GGACCTCTCACACCAAGATCGATGTTTTTGATGGTTCATTGACAATGGAGTTTGATGGTGATGTT
ATTCATCCTAAAATTTCATCTAATTTATCTTTGAAAACTAATGATTTTGTTTGTGTAGTGGAAAA
GTGGGTAAAGAAAGATCGATGTTTTTGATGGTTCATTGACAAT
Found at i:12546 original size:19 final size:19
Alignment explanation
Indices: 12522--12563 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12512 AATGTAGTTG
12522 TTTGCACCTCCAGGGGCAT
1 TTTGCACCTCCAGGGGCAT
** *
12541 TTTGCATGTCCAGGGTCAT
1 TTTGCACCTCCAGGGGCAT
12560 TTTG
1 TTTG
12564 GTCATTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (19 bp):
TTTGCACCTCCAGGGGCAT
Found at i:12578 original size:28 final size:28
Alignment explanation
Indices: 12538--12627 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
12528 CCTCCAGGGG
*
12538 CATTTTGCATGTCCAGGGTCATTTTGGT
1 CATTTTGCATGTCCAGGGGCATTTTGGT
12566 CATTTTGCATGTCCAGGGGCATTTTGGT
1 CATTTTGCATGTCCAGGGGCATTTTGGT
* * *
12594 CATTCTCGCACGTCCAGGGGCATTTTAGT
1 CATT-TTGCATGTCCAGGGGCATTTTGGT
12623 CATTT
1 CATTT
12628 CAAGTACATT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
28 32 0.56
29 25 0.44
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (28 bp):
CATTTTGCATGTCCAGGGGCATTTTGGT
Found at i:13180 original size:25 final size:25
Alignment explanation
Indices: 13151--13226 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
13141 TGGTGGTTTT
13151 ACTCTACATTTACATTTCTTTTTGC
1 ACTCTACATTTACATTTCTTTTTGC
*
13176 ACTCTACTTTTACATTTCTTTTTGC
1 ACTCTACATTTACATTTCTTTTTGC
13201 ACTCTACATTTACATTTC-TTTTGC
1 ACTCTACATTTACATTTCTTTTTGC
13225 AC
1 AC
13227 CAAATGATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 8 0.16
25 41 0.84
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.51
Consensus pattern (25 bp):
ACTCTACATTTACATTTCTTTTTGC
Found at i:13947 original size:17 final size:17
Alignment explanation
Indices: 13925--13959 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13915 CTCAAGCATA
13925 AGCATTTCATCATAAAG
1 AGCATTTCATCATAAAG
13942 AGCATTTCATCATAAAG
1 AGCATTTCATCATAAAG
13959 A
1 A
13960 AACAGTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (17 bp):
AGCATTTCATCATAAAG
Found at i:15450 original size:28 final size:28
Alignment explanation
Indices: 15336--15470 Score: 121
Period size: 27 Copynumber: 4.8 Consensus size: 28
15326 TGAGGTAAGC
* *
15336 TTCTTTTAATTATTTCAATTTCGCCCTT
1 TTCTTTTAATTACTGCAATTTCGCCCTT
* *
15364 TT-TTTTAATTATTGCGATTTCGCCCTT
1 TTCTTTTAATTACTGCAATTTCGCCCTT
* **
15391 TT-TTTTAACTACTGTGATTTCGCCCTTTTTT
1 TTCTTTTAATTACTGCAATTTCGCCC----TT
* *
15422 TTCTTTTAATTACTGCAATTCCGCCTTT
1 TTCTTTTAATTACTGCAATTTCGCCCTT
* *
15450 TTCTTTCAATTGCTGCAATTT
1 TTCTTTTAATTACTGCAATTT
15471 GGGGACTTGT
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
27 45 0.51
28 22 0.25
31 4 0.04
32 18 0.20
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (28 bp):
TTCTTTTAATTACTGCAATTTCGCCCTT
Found at i:23404 original size:3 final size:3
Alignment explanation
Indices: 23396--23424 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23386 ACTCTTTTAA
23396 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23425 GGTTAGTAAC
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:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:26018 original size:23 final size:23
Alignment explanation
Indices: 25988--26037 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
25978 TAACATTTTA
* *
25988 AATATTTTTACATTTTTTTAAAT
1 AATATTTTCACATTTTTATAAAT
* *
26011 AATATTTTCATATTTTTATATAT
1 AATATTTTCACATTTTTATAAAT
26034 AATA
1 AATA
26038 ATCTCTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
AATATTTTCACATTTTTATAAAT
Found at i:26028 original size:21 final size:22
Alignment explanation
Indices: 25983--26037 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
25973 AAAACTAACA
*
25983 TTTTAAAT-AT-TTTTACATTT
1 TTTTAAATAATATTTTACATAT
26003 TTTTAAATAATATTTT-CATAT
1 TTTTAAATAATATTTTACATAT
26024 TTTTATATATAATA
1 TTTTA-A-ATAATA
26038 ATCTCTTGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.27
21 11 0.37
22 5 0.17
23 6 0.20
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAATAATATTTTACATAT
Found at i:26671 original size:16 final size:17
Alignment explanation
Indices: 26645--26676 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
26635 TGTATCTTAT
26645 ATTATATAAATTCATAA
1 ATTATATAAATTCATAA
26662 ATTA-ATAAATTCATA
1 ATTATATAAATTCATA
26677 TATGTATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATATAAATTCATAA
Found at i:31650 original size:2 final size:2
Alignment explanation
Indices: 31643--31690 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
31633 TTATATCATC
* * *
31643 AT AT AT AT AA AT AT AT AC AT AC 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
31685 AT AT AT
1 AT AT AT
31691 CAATCTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31866 original size:2 final size:2
Alignment explanation
Indices: 31859--31886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31849 TGTGTATGTA
31859 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
31887 GTTTTCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38955 original size:26 final size:27
Alignment explanation
Indices: 38871--38970 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
38861 TAGGGTCACC
* *
38871 CAGGGGCATTTTGGTCATTCGTATGTT
1 CAGGGGCATTTTGGTCATTTGTATATT
* * *
38898 CAGGGGCATTTTGGTCATTTTTACACT
1 CAGGGGCATTTTGGTCATTTGTATATT
* *
38925 -AAGGGCATTTTGGTCATTTGCATATT
1 CAGGGGCATTTTGGTCATTTGTATATT
**
38951 CAGGGGCACGTTGGTCATTT
1 CAGGGGCATTTTGGTCATTT
38971 TAAGTCCACT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
26 21 0.36
27 38 0.64
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTGTATATT
Found at i:41810 original size:41 final size:41
Alignment explanation
Indices: 41753--41841 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
41743 GTTCAATATG
*
41753 GTCCCTGATTTAGGATTCTATTTACTATTTGATGCAATTCA
1 GTCCCTGATTTAGGATTCTAGTTACTATTTGATGCAATTCA
* * **
41794 GTCCCTGATTTAGGATTTTAGTTACTATTTGATTCAATTTG
1 GTCCCTGATTTAGGATTCTAGTTACTATTTGATGCAATTCA
41835 GTCCCTG
1 GTCCCTG
41842 GTTTTAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (41 bp):
GTCCCTGATTTAGGATTCTAGTTACTATTTGATGCAATTCA
Found at i:44133 original size:22 final size:21
Alignment explanation
Indices: 44100--44142 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
44090 CAAAATCAAC
* *
44100 TAAAGAAGCAATCAAGAAAAT
1 TAAAGAAACAATCAACAAAAT
*
44121 TAAAGAAAACAATTAACAAAAT
1 TAAAG-AAACAATCAACAAAAT
44143 AGCAGTGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.16
Consensus pattern (21 bp):
TAAAGAAACAATCAACAAAAT
Found at i:50068 original size:23 final size:23
Alignment explanation
Indices: 50042--50089 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
50032 AGGATAGAGT
50042 CTATCATACTCCTCAGAATAAGG
1 CTATCATACTCCTCAGAATAAGG
*
50065 CTATCATACTCCTCAGGATAAGG
1 CTATCATACTCCTCAGAATAAGG
50088 CT
1 CT
50090 TATGGAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (23 bp):
CTATCATACTCCTCAGAATAAGG
Found at i:59161 original size:12 final size:12
Alignment explanation
Indices: 59144--59178 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
59134 CATGACCCGG
59144 CCATGCCGCGCA
1 CCATGCCGCGCA
59156 CCATGCCGCGCA
1 CCATGCCGCGCA
59168 CCATGCCGCGC
1 CCATGCCGCGC
59179 CAACCAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.51, G:0.26, T:0.09
Consensus pattern (12 bp):
CCATGCCGCGCA
Done.