Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015783.1 Corchorus olitorius cultivar O-4 contig15816, 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: 52813
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:502 original size:29 final size:29
Alignment explanation
Indices: 469--546 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
459 ACTTGTAGCG
* *
469 TTTGGATGTTTTGTCCCCTGAATTTCAAT
1 TTTGGACGTTTTGTCCCCTAAATTTCAAT
* * * *
498 TTTGGACATTTTGTTCTCTAAATTTTAAT
1 TTTGGACGTTTTGTCCCCTAAATTTCAAT
527 TTTGGGACGTTTTGTCCCCT
1 TTT-GGACGTTTTGTCCCCT
547 CAGTCTAACG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (29 bp):
TTTGGACGTTTTGTCCCCTAAATTTCAAT
Found at i:2271 original size:13 final size:13
Alignment explanation
Indices: 2253--2277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2243 CTTGCCAAAA
2253 AATAATTTTAAGC
1 AATAATTTTAAGC
2266 AATAATTTTAAG
1 AATAATTTTAAG
2278 GTGGTAAAAA
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:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AATAATTTTAAGC
Found at i:12267 original size:22 final size:22
Alignment explanation
Indices: 12239--12288 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
12229 TGAACAGGGT
12239 GAAAATGGCGCAGAGCCAGAGA
1 GAAAATGGCGCAGAGCCAGAGA
12261 GAAAATGGCGCAGAGCCAGAGA
1 GAAAATGGCGCAGAGCCAGAGA
12283 GAAAAT
1 GAAAAT
12289 AAGCACGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.34, T:0.06
Consensus pattern (22 bp):
GAAAATGGCGCAGAGCCAGAGA
Found at i:15910 original size:5 final size:6
Alignment explanation
Indices: 15895--15946 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
15885 CAACAAAAAT
*
15895 AAAACG AAAACG -AAACA AAAACAG AAAACAG AAAACAG AAAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAAC-G AAAAC-G AAAAC-G -AAAACG AAAACG
15946 A
1 A
15947 TGCCAAACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 4 0.10
6 17 0.41
7 15 0.37
8 5 0.12
ACGTcount: A:0.71, C:0.15, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:15924 original size:7 final size:7
Alignment explanation
Indices: 15895--15936 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
15885 CAACAAAAAT
15895 AAAAC-G
1 AAAACAG
15901 AAAAC-G
1 AAAACAG
15907 -AAACA-
1 AAAACAG
15912 AAAACAG
1 AAAACAG
15919 AAAACAG
1 AAAACAG
15926 AAAACAG
1 AAAACAG
15933 AAAA
1 AAAA
15937 ACGAAAACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 4 0.12
6 11 0.33
7 18 0.55
ACGTcount: A:0.74, C:0.14, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAACAG
Found at i:15942 original size:14 final size:13
Alignment explanation
Indices: 15895--15944 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
15885 CAACAAAAAT
15895 AAAACGAAAAC-G
1 AAAACGAAAACAG
*
15907 -AAACAAAAACAG
1 AAAACGAAAACAG
15919 AAAACAGAAAACAG
1 AAAAC-GAAAACAG
15933 AAAAACGAAAAC
1 -AAAACGAAAAC
15945 GATGCCAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 9 0.28
12 1 0.03
13 4 0.12
14 13 0.41
15 5 0.16
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAACGAAAACAG
Found at i:22637 original size:6 final size:6
Alignment explanation
Indices: 22626--22654 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22616 CAGGGTTTCC
22626 AGCCCG AGCCCG AGCCCG AGCCCG AGCCC
1 AGCCCG AGCCCG AGCCCG AGCCCG AGCCC
22655 TAGGCCACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.52, G:0.31, T:0.00
Consensus pattern (6 bp):
AGCCCG
Found at i:37676 original size:20 final size:20
Alignment explanation
Indices: 37646--37691 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
37636 AATTCACCCA
37646 ACTTATAAAGGCTTATAAAG
1 ACTTATAAAGGCTTATAAAG
* * * *
37666 TCTTATGAAGGGTTATTAAG
1 ACTTATAAAGGCTTATAAAG
37686 ACTTAT
1 ACTTAT
37692 TGAAAGTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (20 bp):
ACTTATAAAGGCTTATAAAG
Found at i:37798 original size:51 final size:51
Alignment explanation
Indices: 37742--37919 Score: 131
Period size: 51 Copynumber: 3.2 Consensus size: 51
37732 ACAAACTTTA
37742 AACTTGCTATTTGAAAGTATTTAATTATCTTAACTTAGCCAAGCTTATCTT
1 AACTTGCTATTTGAAAGTATTTAATTATCTTAACTTAGCCAAGCTTATCTT
* * * * * ** *
37793 AACTTGCTGTTTTAGTTAATTAAGAATTTGAAAGTATATAATTAGCTTAACTTAGCTTAGAAAAC
1 AACTTGCT-ATTT-G---A--AAGTATTT--AA-T-TAT-CTTAACTTAGCCAAGCTT----ATC
37858 TTT
50 -TT
37861 AACTTGCTATTTGAAAGTATTTAATTATCTTAACTTAGCCAAGCTTATCTT
1 AACTTGCTATTTGAAAGTATTTAATTATCTTAACTTAGCCAAGCTTATCTT
37912 AACTTGCT
1 AACTTGCT
37920 GTTTTAGTTA
Statistics
Matches: 94, Mismatches: 16, Indels: 34
0.65 0.11 0.24
Matches are distributed among these distances:
51 18 0.19
52 5 0.05
53 1 0.01
56 14 0.15
57 3 0.03
58 8 0.09
59 2 0.02
60 2 0.02
61 8 0.09
62 3 0.03
63 14 0.15
66 1 0.01
67 5 0.05
68 10 0.11
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (51 bp):
AACTTGCTATTTGAAAGTATTTAATTATCTTAACTTAGCCAAGCTTATCTT
Found at i:37957 original size:120 final size:120
Alignment explanation
Indices: 37713--38087 Score: 691
Period size: 120 Copynumber: 3.1 Consensus size: 120
37703 TTAAAGTCTT
37713 ATTAGCTTAACTTAGCTTA-ACAAACTTTAAACTTGCTATTTGAAAGTATTTAATTATCTTAACT
1 ATTAGCTTAACTTAGCTTAGA-AAACTTT-AACTTGCTATTTGAAAGTATTTAATTATCTTAACT
*
37777 TAGCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAA-GAATTTGAAAGTATATA
64 TAGCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAACAAATTTGAAAGTATATA
37833 ATTAGCTTAACTTAGCTTAGAAAACTTTAACTTGCTATTTGAAAGTATTTAATTATCTTAACTTA
1 ATTAGCTTAACTTAGCTTAGAAAACTTTAACTTGCTATTTGAAAGTATTTAATTATCTTAACTTA
37898 GCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAACAAATTTGAAAGTATATA
66 GCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAACAAATTTGAAAGTATATA
* *
37953 ATTAGCTTAACTTAGCTTAGCAAACTTTAACTTGCTATTTTAAAGTATTTAATTATCTTAACTTA
1 ATTAGCTTAACTTAGCTTAGAAAACTTTAACTTGCTATTTGAAAGTATTTAATTATCTTAACTTA
38018 GCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAACAAATTTGAAAGTATATA
66 GCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAACAAATTTGAAAGTATATA
38073 ATTAGCTTAACTTAG
1 ATTAGCTTAACTTAG
38088 TTAACTTAGT
Statistics
Matches: 250, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
119 74 0.30
120 175 0.70
121 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (120 bp):
ATTAGCTTAACTTAGCTTAGAAAACTTTAACTTGCTATTTGAAAGTATTTAATTATCTTAACTTA
GCCAAGCTTATCTTAACTTGCTGTTTTAGTTAATTAACAAATTTGAAAGTATATA
Found at i:40038 original size:68 final size:72
Alignment explanation
Indices: 39933--40072 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
39923 GGAACTAAAA
* *
39933 TTGCATTGTCAAGAGAAAAGAATGATACATATCTATAAG-A-AGTGTTTGAGAGCAACCTTTAGA
1 TTGCATTGTCAAGAGAAAAGAAGGATACACATCTATAAGAATAGTGTTTGAGAGCAACCTTTAGA
39996 AAAAATT
66 AAAAATT
40003 TTGCATTGTC-A-AGAAAAGAAGGATACACATCTATAAGAATTTAGTGTTTGAGAGCAACCTTTA
1 TTGCATTGTCAAGAGAAAAGAAGGATACACATCTATAAGAA--TAGTGTTTGAGAGCAACCTTTA
40066 GAAAAAA
64 GAAAAAA
40073 AAATTTCATC
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
68 24 0.38
69 2 0.03
70 10 0.16
72 28 0.44
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (72 bp):
TTGCATTGTCAAGAGAAAAGAAGGATACACATCTATAAGAATAGTGTTTGAGAGCAACCTTTAGA
AAAAATT
Found at i:40591 original size:121 final size:121
Alignment explanation
Indices: 40377--40615 Score: 442
Period size: 121 Copynumber: 2.0 Consensus size: 121
40367 AATGTCAATG
40377 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA
1 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA
*
40442 TAGCAATCTTATTGAACTAAAGCTCTAAGTACCACAAATCTGACTCACCAAATTTT
66 TAGCAATCTTATTGAAATAAAGCTCTAAGTACCACAAATCTGACTCACCAAATTTT
*
40498 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGTCTATCTTACTTGAAAGACATAA
1 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA
* *
40563 TAGCAGTCTTATTGAAATAAAGCTCTAAGTACCACAACTCTGACTCACCAAAT
66 TAGCAATCTTATTGAAATAAAGCTCTAAGTACCACAAATCTGACTCACCAAAT
40616 CATGTATGAC
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (121 bp):
GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA
TAGCAATCTTATTGAAATAAAGCTCTAAGTACCACAAATCTGACTCACCAAATTTT
Found at i:41176 original size:2 final size:2
Alignment explanation
Indices: 41163--41203 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
41153 GCAATTCTTT
* *
41163 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41204 TGAAGTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:44610 original size:9 final size:9
Alignment explanation
Indices: 44596--44657 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
44586 GAAGCAATCT
44596 AAAGAAAAA
1 AAAGAAAAA
44605 AAAGAAAAAA
1 AAAG-AAAAA
*
44615 CGAAAGAGAAAGC
1 --AAAGA-AAA-A
44628 AAAGAAAAA
1 AAAGAAAAA
*
44637 AAAG-AGAA
1 AAAGAAAAA
44645 AAAGAAAAA
1 AAAGAAAAA
44654 AAAG
1 AAAG
44658 TAAGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 7 0.16
9 15 0.35
10 8 0.19
11 6 0.14
12 7 0.16
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:44672 original size:19 final size:17
Alignment explanation
Indices: 44596--44657 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
44586 GAAGCAATCT
44596 AAAGAAAAAAAAGA-AA
1 AAAGAAAAAAAAGAGAA
* * *
44612 AAACGAAAGAGAA-AG-C
1 AAA-GAAAAAAAAGAGAA
44628 AAAGAAAAAAAAGAGAA
1 AAAGAAAAAAAAGAGAA
44645 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
44658 TAAGAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
15 7 0.19
16 9 0.25
17 20 0.56
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAGAGAA
Found at i:49744 original size:54 final size:55
Alignment explanation
Indices: 49586--50139 Score: 651
Period size: 54 Copynumber: 10.2 Consensus size: 55
49576 GAACCCTAGA
* * *
49586 TGATCTAGTGCGGTCATTCCAAAGAAGTTTTTAGA-GATCAGAGTTGATC-CCTAGA-
1 TGATCCAGTGCGGTCATTCC-AAGAAGTTTTCA-ATGATCAGAGTTGATCTCC-AAAT
* * * ****
49641 TGATCTAGTGCGGTAATTCCAAAGAAGTTTTTAATGATCAGAGTTGATCTTTTGA-
1 TGATCCAGTGCGGTCATTCC-AAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
* * * *
49696 TGATCTAGTGCAGTCATTCCAAGAAGTTTTCAATGATCATAGTTGATCTCCAGA-
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
* * ** * *
49750 TGATCCAATTCGGTCATTTTAAGAAGTTTTCGATGATCAGAGTTCATCTCC-AAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
* * * *
49804 TGATCCAGTGTGGTCGTTCCAAGAAGTTTTCGATGATCAGAGTTGATCT-TAAAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
* * **
49858 TGATCCAGTGTGGTCGTTCCAAGAAGTTTTTGATGATCAGAGTTGATCTCC-AAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
* * * * *
49912 TGATCCAGTGTGATAATTCCAAGAAATTTTCAATGATTAGAGTTGATCTCCAAAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
49967 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
*
50022 TGATCCACTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCT-CAAAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
* * * * *
50076 TGATCCAGTGTGTTCGTTCCAAGAAGTTTTCGATGATCAGGGTTGATCTCC-AAT
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
50130 TGATCCAGTG
1 TGATCCAGTG
50140 TTGATCGGTC
Statistics
Matches: 442, Mismatches: 50, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.00
54 273 0.62
55 168 0.38
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (55 bp):
TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAAAT
Done.