Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014543.1 Corchorus capsularis cultivar CVL-1 contig14564, 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: 77755
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3388 original size:2 final size:2
Alignment explanation
Indices: 3381--3411 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3371 TCATGGAATA
3381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3412 AGGATTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5981 original size:2 final size:2
Alignment explanation
Indices: 5932--5967 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5922 AGTAACAATC
5932 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
5968 TCAGTACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6546 original size:16 final size:17
Alignment explanation
Indices: 6515--6547 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6505 GCTAGGAATC
*
6515 AAGAGAAGACTCAAGGG
1 AAGAAAAGACTCAAGGG
6532 AAGAAAAGA-TCAAGGG
1 AAGAAAAGACTCAAGGG
6548 CAAAGGTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.09, G:0.33, T:0.06
Consensus pattern (17 bp):
AAGAAAAGACTCAAGGG
Found at i:8373 original size:84 final size:86
Alignment explanation
Indices: 8114--8563 Score: 251
Period size: 84 Copynumber: 5.0 Consensus size: 86
8104 CATCACAGAC
* * * * *
8114 TCGAGTTGGTCTCAATGGAGTGAACCTTTTAAGCAACCCTACTTTCACTACTACTCAGAGTACTA
1 TCGAGTTGGTCCCAAT-G-GTG-AGCTTTTAAGCAACCCTACTCTCAATACTACTCAGA--A-TG
** *
8179 TAACATCACAGCCTCAAATGTCTCAGCTGCT
60 TTGCATCACAGCCTC-AATGTCTCA---ACT
* * * * *
8210 TCGAGGTGGTCTCAATGGAATGAACCTTTTAAGCAACTCTACTGTCACTACTACTACTACTCAGA
1 TCGAGTTGGTCCCAATGG--TG-AGCTTTTAAGCAACCCTAC--T--CT-C-AATACTACTCAGA
* *
8275 GTACTGTTTCATCACAGCCTCAATTTTCTCAACT
57 --A-TGTTGCATCACAGCCTCAA-TGTCTCAACT
8309 TCGAGTTGGTCCCAAT-G-GA-CTTTTAAGCAACCCTACTCTCAA-ATCTACTCAGAATGTTGCA
1 TCGAGTTGGTCCCAATGGTGAGCTTTTAAGCAACCCTACTCTCAATA-CTACTCAGAATGTTGCA
*
8370 TCACAGACTCCAATGTCTCAACT
65 TCACAGCCT-CAATGTCTCAACT
* * * * *
8393 TCGCGTTGGTCCCAATGGAGTGAGGCTTTTAATCCACCCTACTGTCAATACTACTCAGAATATTG
1 TCGAGTTGGTCCCAAT-G-GTGA-GCTTTTAAGCAACCCTACTCTCAATACTACTCAGAATGTTG
8458 CATCACAGCCTC-A-G------CT
63 CATCACAGCCTCAATGTCTCAACT
* * * * *
8474 TCGAGTTGGTCTCAATGAAGCGAATCTTTTAAGCAACAACCCTTCCCTCAA-ATCTACTCAGAAT
1 TCGAGTTGGTCCCAATG--GTG-AGCTTTTAAG---CAACCCTACTCTCAATA-CTACTCAGAAT
8538 GTTGCATCACAGCCTGCAATGTCTCA
59 GTTGCATCACAGCCT-CAATGTCTCA
8564 GCAGCTTGAA
Statistics
Matches: 291, Mismatches: 31, Indels: 68
0.75 0.08 0.17
Matches are distributed among these distances:
80 1 0.00
81 26 0.09
82 1 0.00
83 1 0.00
84 74 0.25
85 5 0.02
86 2 0.01
87 13 0.04
88 4 0.01
89 3 0.01
90 44 0.15
91 2 0.01
93 16 0.05
94 2 0.01
95 2 0.01
96 36 0.12
98 2 0.01
99 16 0.05
100 1 0.00
101 3 0.01
102 37 0.13
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (86 bp):
TCGAGTTGGTCCCAATGGTGAGCTTTTAAGCAACCCTACTCTCAATACTACTCAGAATGTTGCAT
CACAGCCTCAATGTCTCAACT
Found at i:8459 original size:90 final size:84
Alignment explanation
Indices: 8284--8470 Score: 216
Period size: 90 Copynumber: 2.2 Consensus size: 84
8274 AGTACTGTTT
* *
8284 CATCACAGCCTCAATTTTCTCAACTTCGAGTTGGTCCCAATGGACTTTTAAGCAACCCTACTCTC
1 CATCACAGACTCAATTGTCTCAACTTCGAGTTGGTCCCAATGGACTTTTAAGCAACCCTACTCTC
*
8349 AAATCTACTCAGAATGTTG
66 AAATCTACTCAGAATATTG
* * *
8368 CATCACAGACTCCAA-TGTCTCAACTTCGCGTTGGTCCCAATGGAGTGAGGCTTTTAATCCACCC
1 CATCACAGACT-CAATTGTCTCAACTTCGAGTTGGTCCCAAT---G-GA--CTTTTAAGCAACCC
*
8432 TACTGTC-AATACTACTCAGAATATTG
59 TACTCTCAAAT-CTACTCAGAATATTG
*
8458 CATCACAGCCTCA
1 CATCACAGACTCA
8471 GCTTCGAGTT
Statistics
Matches: 87, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
84 34 0.39
85 3 0.03
87 1 0.01
88 2 0.02
89 5 0.06
90 42 0.48
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (84 bp):
CATCACAGACTCAATTGTCTCAACTTCGAGTTGGTCCCAATGGACTTTTAAGCAACCCTACTCTC
AAATCTACTCAGAATATTG
Found at i:8490 original size:81 final size:83
Alignment explanation
Indices: 8386--8552 Score: 187
Period size: 81 Copynumber: 2.0 Consensus size: 83
8376 ACTCCAATGT
* * * * * **
8386 CTCAACTTCGCGTTGGTCCCAATGGAGTGAGGCTTTTAATC-C-ACCCTACTGTC-AATACTACT
1 CTCAACTTCGAGTTGGTCCCAATGAAGCGAAGCTTTTAAGCACAACCCTACCCTCAAAT-CTACT
8448 CAGAATATTGCATCACAGC
65 CAGAATATTGCATCACAGC
* * * *
8467 CTCAGCTTCGAGTTGGTCTCAATGAAGCGAATCTTTTAAGCAACAACCCTTCCCTCAAATCTACT
1 CTCAACTTCGAGTTGGTCCCAATGAAGCGAAGCTTTTAAGC-ACAACCCTACCCTCAAATCTACT
*
8532 CAGAATGTTGCATCACAGC
65 CAGAATATTGCATCACAGC
8551 CT
1 CT
8553 GCAATGTCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
81 33 0.47
83 1 0.01
84 33 0.47
85 3 0.04
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (83 bp):
CTCAACTTCGAGTTGGTCCCAATGAAGCGAAGCTTTTAAGCACAACCCTACCCTCAAATCTACTC
AGAATATTGCATCACAGC
Found at i:8806 original size:1 final size:1
Alignment explanation
Indices: 8800--8845 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
8790 GAACTGTATG
8800 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8846 AATTAATGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10777 original size:2 final size:2
Alignment explanation
Indices: 10766--10799 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10756 AGTTAATAAG
10766 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10800 TTAACTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17560 original size:3 final size:3
Alignment explanation
Indices: 17554--17582 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17544 AAAAAAAGGA
17554 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
17583 ATTAAAAGTC
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:27942 original size:34 final size:35
Alignment explanation
Indices: 27904--27972 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
27894 TTGCAGTTCC
27904 TTTGTTCTTATTCATTACT-AATTCTTTTTTCATA
1 TTTGTTCTTATTCATTACTAAATTCTTTTTTCATA
27938 TTTGTTCTTATTCATTACTAAATTCTTTTTTCATA
1 TTTGTTCTTATTCATTACTAAATTCTTTTTTCATA
27973 ATAATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (35 bp):
TTTGTTCTTATTCATTACTAAATTCTTTTTTCATA
Found at i:29073 original size:15 final size:15
Alignment explanation
Indices: 29053--29082 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29043 GTTCTTATAT
29053 TGTTTAAATCTAATG
1 TGTTTAAATCTAATG
29068 TGTTTAAATCTAATG
1 TGTTTAAATCTAATG
29083 CAGCCCAAAT
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:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TGTTTAAATCTAATG
Found at i:32157 original size:18 final size:18
Alignment explanation
Indices: 32134--32168 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32124 TCCGGGGATC
*
32134 ATGACGATGGAGATAGGG
1 ATGACGATGGAAATAGGG
32152 ATGACGATGGAAATAGG
1 ATGACGATGGAAATAGG
32169 ATGTGGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.40, T:0.17
Consensus pattern (18 bp):
ATGACGATGGAAATAGGG
Found at i:59687 original size:27 final size:27
Alignment explanation
Indices: 59632--59743 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 27
59622 CCAGTGGAGC
* * * *
59632 ATGAGGGCCCAAAGCCTAAGATAGAGA
1 ATGAGGGGCCAAAGCCTGAGGTAGGGA
*
59659 ATGAGGGGCCAAAGCCTGAGGCAGGGA
1 ATGAGGGGCCAAAGCCTGAGGTAGGGA
* *
59686 ATGA-GGGTCAGAAGCCTGATGTAGGGA
1 ATGAGGGGCCA-AAGCCTGAGGTAGGGA
* * *
59713 GTGAGGGTCAAAAGCCTGAGGT-GGAGA
1 ATGAGGGGCCAAAGCCTGAGGTAGG-GA
59740 ATGA
1 ATGA
59744 TACTTCAAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 7 0.10
27 58 0.85
28 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.39, T:0.13
Consensus pattern (27 bp):
ATGAGGGGCCAAAGCCTGAGGTAGGGA
Found at i:59782 original size:54 final size:54
Alignment explanation
Indices: 59723--59874 Score: 153
Period size: 54 Copynumber: 2.8 Consensus size: 54
59713 GTGAGGGTCA
* * * * * * *
59723 AAAGCCTGAGGTGGAGAATGAT-ACTTCAAAGTCCCAGGTGGAGAGTATGGGTTC
1 AAAGCCTCAGCTGGAGAATGATGA-TGCAAAGCCCCAGCTGGAGACTATAGGTTC
* * * *
59777 TAAGCCTCAGCTAGAGAGTGATGATGCAGAGCCCCAGCTGGAGACTATAGGTTC
1 AAAGCCTCAGCTGGAGAATGATGATGCAAAGCCCCAGCTGGAGACTATAGGTTC
* ***
59831 AAAGCCTCAGTTGGAGAATGATGATTTGAAGCCCCAGCTGGAGA
1 AAAGCCTCAGCTGGAGAATGATGATGCAAAGCCCCAGCTGGAGA
59875 ATGCGGGTCT
Statistics
Matches: 78, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
54 77 0.99
55 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (54 bp):
AAAGCCTCAGCTGGAGAATGATGATGCAAAGCCCCAGCTGGAGACTATAGGTTC
Found at i:59875 original size:27 final size:28
Alignment explanation
Indices: 59734--59877 Score: 91
Period size: 27 Copynumber: 5.3 Consensus size: 28
59724 AAGCCTGAGG
* * *
59734 TGGAGAATGATA-CTTCAAAGTCCCAGG
1 TGGAGAATGATAGATTCAAAGCCCCAGC
* * * * *
59761 TGGAGAGT-ATGGGTTCTAAGCCTCAGC
1 TGGAGAATGATAGATTCAAAGCCCCAGC
* * * *
59788 TAGAGAGTGAT-GATGCAGAGCCCCAGC
1 TGGAGAATGATAGATTCAAAGCCCCAGC
* * * *
59815 TGGAGACT-ATAGGTTCAAAGCCTCAGT
1 TGGAGAATGATAGATTCAAAGCCCCAGC
**
59842 TGGAGAATGAT-GATTTGAAGCCCCAGC
1 TGGAGAATGATAGATTCAAAGCCCCAGC
59869 TGGAGAATG
1 TGGAGAATG
59878 CGGGTCTCAA
Statistics
Matches: 87, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
26 4 0.05
27 79 0.91
28 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (28 bp):
TGGAGAATGATAGATTCAAAGCCCCAGC
Found at i:62763 original size:23 final size:23
Alignment explanation
Indices: 62733--62778 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
62723 TCAAGGCTCC
62733 TGTTTTCTGAACCCTTCCTAGCT
1 TGTTTTCTGAACCCTTCCTAGCT
62756 TGTTTTCTGAACCCTTCCTAGCT
1 TGTTTTCTGAACCCTTCCTAGCT
62779 CAAGATGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.43
Consensus pattern (23 bp):
TGTTTTCTGAACCCTTCCTAGCT
Found at i:62833 original size:18 final size:18
Alignment explanation
Indices: 62810--62845 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62800 CTCCATCCCC
62810 CCTCTTAATTTATCATTT
1 CCTCTTAATTTATCATTT
62828 CCTCTTAATTTATCATTT
1 CCTCTTAATTTATCATTT
62846 TACAACTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTCTTAATTTATCATTT
Found at i:62967 original size:14 final size:15
Alignment explanation
Indices: 62948--62977 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62938 TGTTCTAGTG
62948 ATTAAT-AGAGATCA
1 ATTAATCAGAGATCA
62962 ATTAATCAGAGATCA
1 ATTAATCAGAGATCA
62977 A
1 A
62978 ACAGAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (15 bp):
ATTAATCAGAGATCA
Found at i:64642 original size:19 final size:19
Alignment explanation
Indices: 64618--64658 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
64608 TTTTAGTTTA
64618 ATGTTCTTATTATGGATTT
1 ATGTTCTTATTATGGATTT
64637 ATGTTCTTATTATGGATTT
1 ATGTTCTTATTATGGATTT
64656 ATG
1 ATG
64659 GTATGAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (19 bp):
ATGTTCTTATTATGGATTT
Found at i:72390 original size:93 final size:93
Alignment explanation
Indices: 72245--72471 Score: 355
Period size: 93 Copynumber: 2.4 Consensus size: 93
72235 GTTGCCGGAA
* **
72245 TTGCCTACACTTGTACGGGAGGCGCCACTACCGGAGCTGCGACCGACGGAGTTGCCTGCGCCGAA
1 TTGCCTACACTTGGACGGGAGGCGCCACCGCCGGAGCTGCGACCGACGGAGTTGCCTGCGCCGAA
*
72310 GTTGCGACGAAGGGAGGGGCCACCAGAG
66 GTTGCGACGAAGGCAGGGGCCACCAGAG
* * *
72338 TTGCCTACACTTGGACGGGAGGCGCCACCGCTGGAGCTGCGACCGACGGAGTTGCCTGCTCCGGA
1 TTGCCTACACTTGGACGGGAGGCGCCACCGCCGGAGCTGCGACCGACGGAGTTGCCTGCGCCGAA
* *
72403 GTTGCGACGAAGGCAGGGGCCGCCGGAG
66 GTTGCGACGAAGGCAGGGGCCACCAGAG
* *
72431 TTGCCTACACTTGGATGGGAGGCGCCACCGCCGGAGTTGCG
1 TTGCCTACACTTGGACGGGAGGCGCCACCGCCGGAGCTGCG
72472 TCAGAATGAG
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 122 1.00
ACGTcount: A:0.18, C:0.30, G:0.38, T:0.15
Consensus pattern (93 bp):
TTGCCTACACTTGGACGGGAGGCGCCACCGCCGGAGCTGCGACCGACGGAGTTGCCTGCGCCGAA
GTTGCGACGAAGGCAGGGGCCACCAGAG
Found at i:73972 original size:35 final size:38
Alignment explanation
Indices: 73903--73982 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 38
73893 TGGGAGATTT
*
73903 TATATAAAAAACAAAGTTAAAGGAAGCATTGTTGAGAGAA
1 TATATAAAAAACAAAGTTAAAGCAA-CA-TGTTGAGAGAA
73943 TATATAAAAAACAAAGTTAAA-CAA-A-GTTGAGAGAA
1 TATATAAAAAACAAAGTTAAAGCAACATGTTGAGAGAA
73978 TATAT
1 TATAT
73983 TCCCTTATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
35 15 0.38
37 1 0.03
39 2 0.05
40 21 0.54
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (38 bp):
TATATAAAAAACAAAGTTAAAGCAACATGTTGAGAGAA
Done.