Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011863.1 Corchorus olitorius cultivar O-4 contig11896, 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: 44442
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1075 original size:6 final size:6
Alignment explanation
Indices: 1058--1098 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
1048 GTACTTTTTA
1058 ATATAG -TATAG ATATAG ATATAG ATATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG --ATATAG ATATAG ATAT
1099 TTATTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
8 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:1088 original size:14 final size:14
Alignment explanation
Indices: 1058--1098 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1048 GTACTTTTTA
1058 ATATAG-TATAG--
1 ATATAGATATAGAT
1069 ATATAGATATAGAT
1 ATATAGATATAGAT
1083 ATATAGATATAGAT
1 ATATAGATATAGAT
1097 AT
1 AT
1099 TTATTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.22
12 5 0.19
14 16 0.59
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
ATATAGATATAGAT
Found at i:8162 original size:1 final size:1
Alignment explanation
Indices: 8156--8180 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
8146 ATCCTCGTTT
8156 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
8181 CTCGAACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13481 original size:6 final size:6
Alignment explanation
Indices: 13472--13503 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
13462 TCATTCTCAC
13472 ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA AT
1 ATTCCA ATTCCA ATTCCA ATTCCA ATTCCA AT
13504 ACAAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTCCA
Found at i:16344 original size:21 final size:18
Alignment explanation
Indices: 16320--16358 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
16310 TATAAACTAA
16320 TAAAAGTATAATTATCAAATT
1 TAAAAGT-TAA-TAT-AAATT
16341 TAAAAGTTAATATAAATT
1 TAAAAGTTAATATAAATT
16359 GTTTAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 3 0.17
21 7 0.39
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAAAGTTAATATAAATT
Found at i:19552 original size:44 final size:40
Alignment explanation
Indices: 19497--19615 Score: 179
Period size: 38 Copynumber: 2.9 Consensus size: 40
19487 TTGATTTTGA
19497 TTTTATTTAAATTATATATATTATATATGATAAAGTATTTTTAT
1 TTTTATTTAAATTATATATATTATATATGATAAAGTA----TAT
19541 TTTTATTTAAATTATATATATTATATATGATAAAG--TAT
1 TTTTATTTAAATTATATATATTATATATGATAAAGTATAT
*
19579 TTTTATTTAAATTATATATATTATATATTATAAAGTA
1 TTTTATTTAAATTATATATATTATATATGATAAAGTA
19616 ATATATGATA
Statistics
Matches: 72, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
38 37 0.51
44 35 0.49
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (40 bp):
TTTTATTTAAATTATATATATTATATATGATAAAGTATAT
Found at i:21498 original size:17 final size:17
Alignment explanation
Indices: 21455--21489 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21445 TTGCATAATC
21455 CTTTAAATATAGTGTTT
1 CTTTAAATATAGTGTTT
21472 CTTTAAATATAGTGTTT
1 CTTTAAATATAGTGTTT
21489 C
1 C
21490 CTTTGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (17 bp):
CTTTAAATATAGTGTTT
Found at i:22838 original size:22 final size:22
Alignment explanation
Indices: 22813--22998 Score: 150
Period size: 22 Copynumber: 8.5 Consensus size: 22
22803 GGATTATTAA
*
22813 CAAAATCTCATAGGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* **
22835 CAAAA-CTCATAGAAAGGTTA-
1 CAAAATTTCATAGGGAGGTTAT
*
22855 CAAAATTTCATAGGAAGGTTTATT
1 CAAAATTTCATAGGGAGG-TTA-T
* ** *
22879 C-AAATTTTATAGCTATGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
22900 CAAAGTTTCATATGGAGTTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
22922 CATAATTTCATAGGTA-GTTAT
1 CAAAATTTCATAGGGAGGTTAT
22943 CAAAATTTCATAGGGTA-GTTAT
1 CAAAATTTCATAGGG-AGGTTAT
* *
22965 CAAAATTTAATAGGGTA-ATTAT
1 CAAAATTTCATAGGG-AGGTTAT
22987 CAAAATTTCATA
1 CAAAATTTCATA
22999 AAAAAATTCA
Statistics
Matches: 133, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.04
21 42 0.32
22 73 0.55
23 12 0.09
24 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Found at i:22845 original size:21 final size:21
Alignment explanation
Indices: 22812--22874 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
22802 GGGATTATTA
*
22812 ACAAAATCTCATAGGGAGGTT
1 ACAAAATCTCATAGGAAGGTT
*
22833 ATCAAAA-CTCATAGAAAGGTT
1 A-CAAAATCTCATAGGAAGGTT
*
22854 ACAAAATTTCATAGGAAGGTT
1 ACAAAATCTCATAGGAAGGTT
22875 TATTCAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.14
21 26 0.72
22 5 0.14
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (21 bp):
ACAAAATCTCATAGGAAGGTT
Found at i:22949 original size:65 final size:66
Alignment explanation
Indices: 22855--22998 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 66
22845 AGAAAGGTTA
* * *
22855 CAAAATTTCATAGGAAGGTTTATTCAAATTTTATA-GCTATGTTATCAAAGTTTCATATGGAGT-
1 CAAAATTTCATAGGAAGGTTTATTCAAATTTCATAGGCTA-GTTATCAAAATTTAATA-GG-GTA
22918 TTAT
63 TTAT
* * *
22922 CATAATTTCATAGGTA-G-TTA-TCAAAATTTCATAGGGTAGTTATCAAAATTTAATAGGGTAAT
1 CAAAATTTCATAGGAAGGTTTATTC-AAATTTCATAGGCTAGTTATCAAAATTTAATAGGGT-AT
22984 TAT
64 TAT
22987 CAAAATTTCATA
1 CAAAATTTCATA
22999 AAAAAATTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
63 2 0.03
64 4 0.06
65 42 0.64
66 4 0.06
67 14 0.21
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (66 bp):
CAAAATTTCATAGGAAGGTTTATTCAAATTTCATAGGCTAGTTATCAAAATTTAATAGGGTATTA
T
Found at i:24149 original size:13 final size:13
Alignment explanation
Indices: 24114--24149 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
24104 CCCTAAAATT
24114 TTGTCTATCATCC
1 TTGTCTATCATCC
*
24127 TTGTGT-TCATCC
1 TTGTCTATCATCC
24139 TTGTCTATCAT
1 TTGTCTATCAT
24150 TCTGTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.14, C:0.25, G:0.11, T:0.50
Consensus pattern (13 bp):
TTGTCTATCATCC
Found at i:25669 original size:16 final size:16
Alignment explanation
Indices: 25650--25680 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25640 AACCGAAAAA
25650 GACTCGAACCAAAATT
1 GACTCGAACCAAAATT
*
25666 GACTCGAACCCAAAT
1 GACTCGAACCAAAAT
25681 GACCCGACAT
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:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (16 bp):
GACTCGAACCAAAATT
Found at i:29632 original size:17 final size:17
Alignment explanation
Indices: 29591--29633 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29581 TTTTCTAACC
*
29591 ATTATTATTGAGCTAATA
1 ATTATTA-TGAACTAATA
* *
29609 ATAATTATGAACTAATT
1 ATTATTATGAACTAATA
29626 ATTATTAT
1 ATTATTAT
29634 TCAATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTATTATGAACTAATA
Found at i:32123 original size:2 final size:2
Alignment explanation
Indices: 32116--32142 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32106 TAATATGTAG
32116 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 T
32143 TATCATGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36949 original size:13 final size:12
Alignment explanation
Indices: 36927--36956 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
36917 GGGGCTTTGA
36927 TTTTTCTTTTTC
1 TTTTTCTTTTTC
36939 TTTTTCTTTTTTC
1 TTTTTC-TTTTTC
36952 TTTTT
1 TTTTT
36957 TGGGTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:36957 original size:7 final size:6
Alignment explanation
Indices: 36927--36956 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
36917 GGGGCTTTGA
36927 TTTTTC TTTTTC TTTTTC TTTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC -TTTTTC TTTTT
36957 TGGGTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:41675 original size:33 final size:33
Alignment explanation
Indices: 41633--41698 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41623 ACCAGTAATC
41633 TTACCAAAATCTTGTTTGGTTCGCTTGTAGGAA
1 TTACCAAAATCTTGTTTGGTTCGCTTGTAGGAA
41666 TTACCAAAATCTTGTTTGGTTCGCTTGTAGGAA
1 TTACCAAAATCTTGTTTGGTTCGCTTGTAGGAA
41699 ATGCAGTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (33 bp):
TTACCAAAATCTTGTTTGGTTCGCTTGTAGGAA
Found at i:41746 original size:38 final size:38
Alignment explanation
Indices: 41695--41772 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
41685 TTCGCTTGTA
41695 GGAAATGCAGTGGGAATATTTGATTACCTTGTTTGGTT
1 GGAAATGCAGTGGGAATATTTGATTACCTTGTTTGGTT
41733 GGAAATGCAGTGGGAATATTTGATTACCTTGTTTGGTT
1 GGAAATGCAGTGGGAATATTTGATTACCTTGTTTGGTT
41771 GG
1 GG
41773 GTGGGAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (38 bp):
GGAAATGCAGTGGGAATATTTGATTACCTTGTTTGGTT
Found at i:42497 original size:51 final size:51
Alignment explanation
Indices: 42419--42517 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
42409 AAAGTATAGG
42419 AAAGAAAATAAAAAATAATGAAAGGGAGAAGATTGGTCTTCGTCTCTTACT
1 AAAGAAAATAAAAAATAATGAAAGGGAGAAGATTGGTCTTCGTCTCTTACT
*
42470 AAAGAAAATAAAAAATAATGAATGGGAGAAGATTGGTCTTCGTCTCTT
1 AAAGAAAATAAAAAATAATGAAAGGGAGAAGATTGGTCTTCGTCTCTT
42518 TAAATGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.26
Consensus pattern (51 bp):
AAAGAAAATAAAAAATAATGAAAGGGAGAAGATTGGTCTTCGTCTCTTACT
Done.