Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019703.1 Corchorus olitorius cultivar O-4 contig19736, 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: 37130
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Found at i:748 original size:308 final size:308
Alignment explanation
Indices: 170--771 Score: 961
Period size: 308 Copynumber: 2.0 Consensus size: 308
160 AAAACCGTGA
* * *
170 TGGTTAATTATAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAATATTTATCCTC
1 TGGTTAATTATAATACACGATTTCGACTAAAATTTTACAAAAATTGACACGAAAGATTTATCCTC
* * * *
235 AATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGCCAAAAAGACGAGGGCTTTTCACG
66 AATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGCAAAAAAGACAAGGACATTTCACG
* * * * *
300 CTTTTAATATCTTATTACTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAATAAGATTCAAA
131 ATTTTAATATCGTATTACTTATTTTTCCTAAATTAAATTCTAATTAAATCGAAACAAGATTCAAA
* * * **
365 TACTCGTAAAAGCAAATTCTTAAATCCAATGTTGCTGAGCTTTGGTTAGATGATGTAAAGTATTA
196 TACTCGTAAAAACAAATTATTAAATCCAATCTAACTGAGCTTTGGTTAGATGATGTAAAGTATTA
*
430 AACTAATTTTTTTATTTTTTTAGAAAGAATATTGCTCAAGTACTGCTT
261 AACCAATTTTTTTATTTTTTTAGAAAGAATATTGCTCAAGTACTGCTT
* * * *
478 TGGTTAGTTATAATACACGATTTCGACTAAAATTTTGCAAAAATTGACATGAAAGATTTCTCCTC
1 TGGTTAATTATAATACACGATTTCGACTAAAATTTTACAAAAATTGACACGAAAGATTTATCCTC
543 AATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGCAAAAAAGACAAGGACATTTCACG
66 AATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGCAAAAAAGACAAGGACATTTCACG
*
608 ATTTTAATATCGTATTACTTATTTTTCCTAAATTAAATTCTAATTAAATCGAAACAAGATTCAGA
131 ATTTTAATATCGTATTACTTATTTTTCCTAAATTAAATTCTAATTAAATCGAAACAAGATTCAAA
* * *
673 TCCTTGTAAAAACAAATTATTAAATCCAATCTAACTGAGTTTTGGTTAGATGATGTAAAGTATTA
196 TACTCGTAAAAACAAATTATTAAATCCAATCTAACTGAGCTTTGGTTAGATGATGTAAAGTATTA
*
738 AACCAATTTTTTTATTTTTTTGGAAAGAATATTG
261 AACCAATTTTTTTATTTTTTTAGAAAGAATATTG
772 AAACACTGCT
Statistics
Matches: 267, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
308 267 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (308 bp):
TGGTTAATTATAATACACGATTTCGACTAAAATTTTACAAAAATTGACACGAAAGATTTATCCTC
AATTTTTGGCTAAAATACTCATAAAAATATATAATTCAACGCAAAAAAGACAAGGACATTTCACG
ATTTTAATATCGTATTACTTATTTTTCCTAAATTAAATTCTAATTAAATCGAAACAAGATTCAAA
TACTCGTAAAAACAAATTATTAAATCCAATCTAACTGAGCTTTGGTTAGATGATGTAAAGTATTA
AACCAATTTTTTTATTTTTTTAGAAAGAATATTGCTCAAGTACTGCTT
Found at i:2221 original size:22 final size:22
Alignment explanation
Indices: 2193--2235 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2183 GTAATTTACA
2193 TTATATAACCACTTTACATATG
1 TTATATAACCACTTTACATATG
*
2215 TTATATAGCCACTTTACATAT
1 TTATATAACCACTTTACATAT
2236 AACAACAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (22 bp):
TTATATAACCACTTTACATATG
Found at i:12464 original size:2 final size:2
Alignment explanation
Indices: 12457--12499 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12447 TTAACTTATG
12457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12499 T
1 T
12500 CTTCTTCCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12971 original size:41 final size:41
Alignment explanation
Indices: 12926--13006 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
12916 TTGACCCTTA
* *
12926 TAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCCCTC
1 TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCCCTC
*
12967 TAATAATTAAGGTAAGAAATTAAATCCAGGTTTAACCCCT
1 TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCCCT
13007 AGTTATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (41 bp):
TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCCCTC
Found at i:15284 original size:6 final size:6
Alignment explanation
Indices: 15251--15296 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
15241 TTATCTATTG
* *
15251 TTTTTC TTTCTC TTTTGTC -TTTTC -TTTTC TTTTTC TTTTTA TTTTT
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
15297 TATAAAAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 7 0.20
6 26 0.74
7 2 0.06
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:15996 original size:19 final size:20
Alignment explanation
Indices: 15967--16004 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
15957 TAATTAATTG
15967 TTATAATATTAAATTTTTAT
1 TTATAATATTAAATTTTTAT
15987 TTAT-ATATTAAATTTTTA
1 TTATAATATTAAATTTTTA
16005 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATAATATTAAATTTTTAT
Found at i:16015 original size:19 final size:19
Alignment explanation
Indices: 15974--16015 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
15964 TTGTTATAAT
* * *
15974 ATTAAATTTTTATTTATAT
1 ATTAAATTTTTACTTAAAA
15993 ATTAAATTTTTACTTAAAA
1 ATTAAATTTTTACTTAAAA
16012 ATTA
1 ATTA
16016 CTCATAATCA
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:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAAATTTTTACTTAAAA
Found at i:16767 original size:18 final size:18
Alignment explanation
Indices: 16741--16783 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16731 CATTAGTATC
*
16741 AAAATATATCA-TTATAAA
1 AAAAAATATCACTTA-AAA
16759 AAAAAATATCACTTAAAA
1 AAAAAATATCACTTAAAA
*
16777 AACAAAT
1 AAAAAAT
16784 TTGTGTTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATATCACTTAAAA
Found at i:17161 original size:13 final size:13
Alignment explanation
Indices: 17140--17176 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
17130 GATAATTCTT
17140 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
17153 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
17166 CTTGACCCTCC
1 TTTGACCCTCC
17177 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:17237 original size:40 final size:40
Alignment explanation
Indices: 17175--17251 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
17165 ACTTGACCCT
* *
17175 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
*
17215 CCTAATAATTAAGGTAAGAAATTAAATCCAGATTTAG
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAG
17252 TTCTCAGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
Found at i:18525 original size:24 final size:24
Alignment explanation
Indices: 18497--18546 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
18487 TGAAAATTTA
18497 GATCTCGAGTTTGAATCGTGAAAC
1 GATCTCGAGTTTGAATCGTGAAAC
18521 GATCTCGAGTTTGAATCGTGAAAC
1 GATCTCGAGTTTGAATCGTGAAAC
18545 GA
1 GA
18547 ATAGTGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (24 bp):
GATCTCGAGTTTGAATCGTGAAAC
Found at i:25289 original size:2 final size:2
Alignment explanation
Indices: 25223--25274 Score: 59
Period size: 2 Copynumber: 25.0 Consensus size: 2
25213 CAGGCTCATG
* * *
25223 TA TA TA TA TG TT TA GA TA TA TCA TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA
25267 TA TA TA TA
1 TA TA TA TA
25275 ATGCATCATA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
2 39 0.89
3 5 0.11
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25918 original size:16 final size:16
Alignment explanation
Indices: 25897--25927 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25887 ATTATAATAA
25897 TAATATATACATATAG
1 TAATATATACATATAG
*
25913 TAATATATATATATA
1 TAATATATACATATA
25928 TATAGTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATATATACATATAG
Found at i:29723 original size:36 final size:36
Alignment explanation
Indices: 29683--29757 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
29673 GAAAAAAAAT
29683 AGACTAGCTATCTTAATCCTCGTAAAAAGTTGATTG
1 AGACTAGCTATCTTAATCCTCGTAAAAAGTTGATTG
*
29719 AGACTAGTTATCTTAATCCTCGTAAAAAGTTGATTG
1 AGACTAGCTATCTTAATCCTCGTAAAAAGTTGATTG
29755 AGA
1 AGA
29758 TCTTTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (36 bp):
AGACTAGCTATCTTAATCCTCGTAAAAAGTTGATTG
Found at i:31923 original size:25 final size:25
Alignment explanation
Indices: 31895--31969 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
31885 AAATTCTTAT
31895 TTGATGAACATATAGGCATGTCTAA
1 TTGATGAACATATAGGCATGTCTAA
* * *
31920 TTGAT-TA-AT-TA--AAT-TCTTAT
1 TTGATGAACATATAGGCATGTC-TAA
31940 TTGATGAACATATAGGCATGTCTAA
1 TTGATGAACATATAGGCATGTCTAA
31965 TTGAT
1 TTGAT
31970 TAATTATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
19 2 0.05
20 9 0.24
21 1 0.03
22 4 0.11
23 4 0.11
24 1 0.03
25 14 0.38
26 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (25 bp):
TTGATGAACATATAGGCATGTCTAA
Found at i:31935 original size:45 final size:45
Alignment explanation
Indices: 31882--31975 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
31872 TAATGACTTC
31882 ATTAAATTCTTATTTGATGAACATATAGGCATGTCTAATTGATTA
1 ATTAAATTCTTATTTGATGAACATATAGGCATGTCTAATTGATTA
31927 ATTAAATTCTTATTTGATGAACATATAGGCATGTCTAATTGATTA
1 ATTAAATTCTTATTTGATGAACATATAGGCATGTCTAATTGATTA
31972 ATTA
1 ATTA
31976 TGAATTTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (45 bp):
ATTAAATTCTTATTTGATGAACATATAGGCATGTCTAATTGATTA
Found at i:36782 original size:15 final size:15
Alignment explanation
Indices: 36762--36791 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36752 CCCAACATAA
36762 AAACATGAATCCATC
1 AAACATGAATCCATC
36777 AAACATGAATCCATC
1 AAACATGAATCCATC
36792 CAAAGATTAT
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:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
AAACATGAATCCATC
Done.