Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020815.1 Corchorus olitorius cultivar O-4 contig20848, 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: 61165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2981 original size:10 final size:10
Alignment explanation
Indices: 2966--2999 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2956 ATAATTATCC
*
2966 ATATATATAT
1 ATATATATGT
2976 ATATATATGT
1 ATATATATGT
*
2986 ATGTATATGT
1 ATATATATGT
2996 ATAT
1 ATAT
3000 GTTTATTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:10863 original size:19 final size:19
Alignment explanation
Indices: 10839--10876 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
10829 TCCTGTCGGT
10839 TGCTAAT-CTCATTAGATTA
1 TGCTAATGCTCATT-GATTA
10858 TGCTAATGCTCATTGATTA
1 TGCTAATGCTCATTGATTA
10877 GGTTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (19 bp):
TGCTAATGCTCATTGATTA
Found at i:11015 original size:26 final size:26
Alignment explanation
Indices: 10966--11015 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
10956 GCTACTCTAA
* * *
10966 TAATCTTATCTGTACAGTATCTAATC
1 TAATCTAATCCGTACAGTAGCTAATC
*
10992 TAATCTAATCCGTACAGTCGCTAA
1 TAATCTAATCCGTACAGTAGCTAA
11016 ACAGTGTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (26 bp):
TAATCTAATCCGTACAGTAGCTAATC
Found at i:17751 original size:2 final size:2
Alignment explanation
Indices: 17744--17779 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17734 CTAATTAGAC
17744 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
17780 GGAGAGAAAG
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:18532 original size:19 final size:20
Alignment explanation
Indices: 18490--18547 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
18480 TTGACATTGT
18490 TTAGCAACTGTACAGATGAAA
1 TTAGC-ACTGTACAGATGAAA
* *
18511 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAAA
*
18530 TTAGGTACTGTACAGATG
1 TTA-GCACTGTACAGATG
18548 GGATTATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.52
20 1 0.03
21 14 0.45
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAAA
Found at i:29170 original size:6 final size:6
Alignment explanation
Indices: 29161--29193 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29151 TAAAAAAGAA
*
29161 AAAAAG AAAAAT AAAAAG AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
29194 GATAGAGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:29176 original size:12 final size:11
Alignment explanation
Indices: 29159--29193 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
29149 TATAAAAAAG
29159 AAAAAAAGAAA
1 AAAAAAAGAAA
29170 AATAAAAAGAAA
1 AA-AAAAAGAAA
*
29182 AAGAAAAGAAA
1 AAAAAAAGAAA
29193 A
1 A
29194 GATAGAGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:29957 original size:31 final size:33
Alignment explanation
Indices: 29909--29969 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
29899 TACAAAAAAC
*
29909 TGTCAATTTGGTCCCTCTA-TTTACAAAATTGG
1 TGTCAATTTGGTCCCTCTACTTAACAAAATTGG
29941 TGTCAA-TTGAGT-CCTCTACTTAACAAAAT
1 TGTCAATTTG-GTCCCTCTACTTAACAAAAT
29970 CTGTCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (33 bp):
TGTCAATTTGGTCCCTCTACTTAACAAAATTGG
Found at i:31899 original size:21 final size:22
Alignment explanation
Indices: 31873--31917 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
31863 CACAACAATA
31873 ATTTAGTT-AAAAAATGAATTG
1 ATTTAGTTAAAAAAATGAATTG
31894 ATTTAGTTAAAAAAAATGAATTG
1 ATTTAGTT-AAAAAAATGAATTG
31917 A
1 A
31918 ATGACAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (22 bp):
ATTTAGTTAAAAAAATGAATTG
Found at i:37469 original size:16 final size:16
Alignment explanation
Indices: 37448--37480 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
37438 AGTTTTCATC
37448 GAGTTCGATATTTAAG
1 GAGTTCGATATTTAAG
37464 GAGTTCGATATTTAAG
1 GAGTTCGATATTTAAG
37480 G
1 G
37481 CAAATTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (16 bp):
GAGTTCGATATTTAAG
Found at i:38038 original size:29 final size:30
Alignment explanation
Indices: 37978--38038 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
37968 AACTAGTCTG
*
37978 AAACTAATATATTGATGATCCAATTATCAA
1 AAACTAATATAATGATGATCCAATTATCAA
38008 AAACTAATATAATG-TGATCCAA-TATCAA
1 AAACTAATATAATGATGATCCAATTATCAA
38036 AAA
1 AAA
38039 GTTTATAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 9 0.30
29 8 0.27
30 13 0.43
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.30
Consensus pattern (30 bp):
AAACTAATATAATGATGATCCAATTATCAA
Found at i:38687 original size:29 final size:28
Alignment explanation
Indices: 38645--38702 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
38635 TTTAAGATTT
38645 AAACCCAAATTCTTCAACTACTAAAAAAA
1 AAACCCAAATTCTTCAACTAC-AAAAAAA
* *
38674 AAACCCAAATTCTTCATCTACAAACAAA
1 AAACCCAAATTCTTCAACTACAAAAAAA
38702 A
1 A
38703 GGTTGTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (28 bp):
AAACCCAAATTCTTCAACTACAAAAAAA
Found at i:51971 original size:19 final size:19
Alignment explanation
Indices: 51960--51996 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51950 AATTTTTAAG
51960 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
51979 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
51997 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:56608 original size:20 final size:20
Alignment explanation
Indices: 56583--56622 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56573 TTAGGTTCAA
56583 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
56603 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
56623 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:60437 original size:24 final size:24
Alignment explanation
Indices: 60409--60455 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
60399 TTTATCTCTA
*
60409 AAAAATAATGTGTATTATTTCACCC
1 AAAAA-AATGTGTATTAATTCACCC
60434 AAAAAAATGTGTATTAATTCAC
1 AAAAAAATGTGTATTAATTCAC
60456 AATTCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (24 bp):
AAAAAAATGTGTATTAATTCACCC
Done.