Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016279.1 Corchorus olitorius cultivar O-4 contig16312, 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: 42408
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1001 original size:22 final size:22
Alignment explanation
Indices: 921--1092 Score: 124
Period size: 22 Copynumber: 7.9 Consensus size: 22
911 TCTTAGACAG
*
921 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
942 AGGTTA-CAAATTTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* **
963 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATAGGA
*
986 AGGTTATCAAAGTTTCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
* *
1008 AGTTTATCACAATTTCATAGGTA
1 AGGTTATCAAAATTTCATAGG-A
* *
1031 A-ATCATCAAAATTTCATA--A
1 AGGTTATCAAAATTTCATAGGA
* * *
1050 TGTGATTATCAAAATTTAATAGGGT
1 AG-G-TTATCAAAATTTCATA-GGA
1075 A-GTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
1093 AAAATATTCA
Statistics
Matches: 117, Mismatches: 22, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.01
20 4 0.03
21 19 0.16
22 76 0.65
23 17 0.15
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:1013 original size:44 final size:44
Alignment explanation
Indices: 924--1092 Score: 152
Period size: 44 Copynumber: 3.9 Consensus size: 44
914 TAGACAGAGG
* * *
924 TTATCAAAA-ATCATAGGAAGGTTA-CAAATTTTCATA-GGAAGGT
1 TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGG-A-GT
* * *
967 TTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGAGT
1 TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAGT
* ** *
1011 TTATCACAATTTCATAGGTAAATCATCAAAATTTCATAATGTGA--
1 TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCAT-ATG-GAGT
*
1055 TTATCAAAATTTAATAGGGTA-GTTATCAAAATTTCATA
1 TTATCAAAATTTCATA-GGTAGGTTATCAAAATTTCATA
1093 AAAATATTCA
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
43 9 0.09
44 72 0.69
45 19 0.18
46 4 0.04
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATATGGAGT
Found at i:4971 original size:24 final size:27
Alignment explanation
Indices: 4916--4975 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 27
4906 AATAAATAAA
* *
4916 AACATTCTTTCTTTAAAACAAATAATC
1 AACATACTTACTTTAAAACAAATAATC
4943 AACATACTTACTTT-AAA-AAA-AATC
1 AACATACTTACTTTAAAACAAATAATC
4967 AACATACTT
1 AACATACTT
4976 GTTTCTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 13 0.42
25 3 0.10
26 3 0.10
27 12 0.39
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (27 bp):
AACATACTTACTTTAAAACAAATAATC
Found at i:4993 original size:31 final size:31
Alignment explanation
Indices: 4958--5017 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4948 ACTTACTTTA
4958 AAAAAAATCAACATACTTGTT-TCTCAAAAAT
1 AAAAAAATCAACATACTTGTTATC-CAAAAAT
** *
4989 AAAAATTTCAACATGCTTGTTATCCAAAA
1 AAAAAAATCAACATACTTGTTATCCAAAA
5018 TTTGTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.30
Consensus pattern (31 bp):
AAAAAAATCAACATACTTGTTATCCAAAAAT
Found at i:17593 original size:16 final size:16
Alignment explanation
Indices: 17572--17618 Score: 78
Period size: 15 Copynumber: 2.9 Consensus size: 16
17562 CCAATAAGGG
17572 TTTTTTTTTAAAATTT
1 TTTTTTTTTAAAATTT
17588 TTTTTTTTT-AAATTT
1 TTTTTTTTTAAAATTT
17603 TTTTTTTTTATAAATT
1 TTTTTTTTTA-AAATT
17619 ACTTTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.52
16 9 0.31
17 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTAAAATTT
Found at i:19116 original size:2 final size:2
Alignment explanation
Indices: 19111--19141 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19101 TCTCTCTATC
19111 TA 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 T
19142 TCCTAAGGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33912 original size:13 final size:14
Alignment explanation
Indices: 33884--33922 Score: 62
Period size: 13 Copynumber: 2.8 Consensus size: 14
33874 CCCAGAAAGG
33884 AGAAAGAAACATTAA
1 AGAAA-AAACATTAA
33899 AGAAAAAA-ATTAA
1 AGAAAAAACATTAA
33912 AGAAAAAACAT
1 AGAAAAAACAT
33923 AATCACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.57
14 5 0.22
15 5 0.22
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.13
Consensus pattern (14 bp):
AGAAAAAACATTAA
Found at i:37300 original size:55 final size:55
Alignment explanation
Indices: 37238--37348 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
37228 ATGGTCCTCA
37238 TGGGTGTGTGTGATTGTTTGGTTTGATGTTTGCTTTGGTAGATGTGATTGTTGGT
1 TGGGTGTGTGTGATTGTTTGGTTTGATGTTTGCTTTGGTAGATGTGATTGTTGGT
37293 TGGGTGTGTGTGATTGTTTGGTTTGATGTTTGCTTTGGTAGATGTGATTGTTGGT
1 TGGGTGTGTGTGATTGTTTGGTTTGATGTTTGCTTTGGTAGATGTGATTGTTGGT
37348 T
1 T
37349 TGTAGAGACC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.09, C:0.02, G:0.38, T:0.51
Consensus pattern (55 bp):
TGGGTGTGTGTGATTGTTTGGTTTGATGTTTGCTTTGGTAGATGTGATTGTTGGT
Found at i:40949 original size:39 final size:40
Alignment explanation
Indices: 40893--40973 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
40883 TTTAATTCCT
40893 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
40933 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
40972 AT
1 AT
40974 TCATAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.