Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009842.1 Corchorus olitorius cultivar O-4 contig09874, 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: 7674
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Found at i:1782 original size:22 final size:21
Alignment explanation
Indices: 1738--1816 Score: 106
Period size: 22 Copynumber: 3.7 Consensus size: 21
1728 AGCTCCCTAC
*
1738 GAAAATTTGATAACCACAC-T
1 GAAATTTTGATAACCACACGT
1758 GAAATTTTGATAACCACACAGT
1 GAAATTTTGATAACCACAC-GT
*
1780 GAAATTCTGATAACCACACTGT
1 GAAATTTTGATAACCACAC-GT
*
1802 GAAATTTTGAAAACC
1 GAAATTTTGATAACC
1817 TCAAACACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
20 18 0.35
22 34 0.65
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (21 bp):
GAAATTTTGATAACCACACGT
Found at i:3261 original size:22 final size:22
Alignment explanation
Indices: 3231--3286 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3221 GGAGGTTATA
* * *
3231 AAAAATTCATATTGTGGTTACC
1 AAAATTTCATATTGCGCTTACC
* *
3253 CAAATTTCATAATGCGCTTACC
1 AAAATTTCATATTGCGCTTACC
3275 AAAATTTCATAT
1 AAAATTTCATAT
3287 GAAGGTTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
AAAATTTCATATTGCGCTTACC
Found at i:3299 original size:22 final size:22
Alignment explanation
Indices: 3274--3345 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
3264 ATGCGCTTAC
*
3274 CAAAATTTCATATGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
3296 CAAAATTT-ATAGGGATTAGGTTA-
1 CAAAATTTCATA-GGA--AGGTTAT
*
3319 CTAAAATTTCAAAGGAAGGTTAT
1 C-AAAATTTCATAGGAAGGTTAT
3342 CAAA
1 CAAA
3346 TTTTTCTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
21 3 0.07
22 19 0.45
23 2 0.05
24 16 0.38
25 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:3528 original size:22 final size:22
Alignment explanation
Indices: 3485--3531 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3475 GAAATTTATT
* * *
3485 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGGGAGGCTATC
3507 AAAATTTCATAGGGAGGCTATC
1 AAAATTTCATAGGGAGGCTATC
3529 AAA
1 AAA
3532 GAGGTTATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGCTATC
Found at i:3560 original size:22 final size:22
Alignment explanation
Indices: 3532--3799 Score: 116
Period size: 22 Copynumber: 11.8 Consensus size: 22
3522 GGCTATCAAA
*
3532 GAGGTTATCAAAATTCCATAGC
1 GAGGTTATCAAAATTTCATAGC
* *
3554 GAGGTTATCAGAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGC
* * *
3576 GTGGTTACCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGC
* * *
3598 AATGTTATAAAATTCTAAATTTCATA-C
1 GA-GGT-T---A-TCAAAATTTCATAGC
* * *
3625 GAATGTTATCAAAATTTTATAGT
1 G-AGGTTATCAAAATTTCATAGC
*
3648 GTGGTTATCAAAATTTCATCAG-
1 GAGGTTATCAAAATTTCAT-AGC
* ** * *
3670 GAAGCAATCAAAATCTCATAGA
1 GAGGTTATCAAAATTTCATAGC
* *
3692 GTA-GTTATCAAAAATTCATAGA
1 G-AGGTTATCAAAATTTCATAGC
* * *
3714 GATCAGATTACCAAAATTGCATAG-
1 G---AGGTTATCAAAATTTCATAGC
**
3738 GAAGGTTATCAAAA-TTCATAAT
1 G-AGGTTATCAAAATTTCATAGC
* *
3760 GCGGTTATCAAAATTTTATAG-
1 GAGGTTATCAAAATTTCATAGC
*
3781 GAAGGTTATCAGAATTTCA
1 G-AGGTTATCAAAATTTCA
3800 CAGTGTGATT
Statistics
Matches: 183, Mismatches: 46, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
21 19 0.10
22 125 0.68
23 7 0.04
24 3 0.02
25 14 0.08
26 1 0.01
27 2 0.01
28 12 0.07
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGC
Found at i:3629 original size:28 final size:29
Alignment explanation
Indices: 3586--3640 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
3576 GTGGTTACCA
3586 AAATTTCATAGTAATGTTAT-AAAATTCT
1 AAATTTCATAGTAATGTTATCAAAATTCT
3614 AAATTTCATACG-AATGTTATCAAAATT
1 AAATTTCATA-GTAATGTTATCAAAATT
3641 TTATAGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (29 bp):
AAATTTCATAGTAATGTTATCAAAATTCT
Found at i:3660 original size:72 final size:76
Alignment explanation
Indices: 3480--3681 Score: 218
Period size: 72 Copynumber: 2.7 Consensus size: 76
3470 CATAGGAAAT
* *
3480 TTATTAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGGAGGCTATCAAAGAGGTTATCAAAA
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGAAGGCTATCAAAGA-G-TATCAAAA
3545 TTCCATAGCGAGG
64 TTCCATAGCGAGG
* * * * * *
3558 TTATCAGAATTTCATAGTGTGGTTACCAAAATTTCATAGTAATGTTAT-AAA-A-T-TCTAAATT
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGAAGGCTATCAAAGAGTATCAAAATT
* *
3619 TCATA-CGAATG
66 CCATAGCG-AGG
* *
3630 TTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATCAGGAA-GCAATCAAA
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAT-AGGAAGGCTATCAAA
3682 ATCTCATAGA
Statistics
Matches: 105, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
71 2 0.02
72 50 0.48
73 8 0.08
76 1 0.01
77 3 0.03
78 41 0.39
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (76 bp):
TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGAAGGCTATCAAAGAGTATCAAAATT
CCATAGCGAGG
Found at i:3939 original size:22 final size:22
Alignment explanation
Indices: 3816--3942 Score: 62
Period size: 22 Copynumber: 5.7 Consensus size: 22
3806 GATTACTAAG
* *
3816 ATTTCATAGGGAGGTTATAAAAA
1 ATTTCATAGGGATGTTA-ACAAA
* * * *
3839 ATATCATAGTG-TGCTTACCAAC
1 ATTTCATAGGGATG-TTAACAAA
* * * *
3861 ATTTCACATGGATATTATCAAA
1 ATTTCATAGGGATGTTAACAAA
* ** **
3883 ATTTTATAGTAATGTTTTCAAA
1 ATTTCATAGGGATGTTAACAAA
3905 ATTT--TACGAGGATGTTAACAAA
1 ATTTCATA-G-GGATGTTAACAAA
3927 ATTTCATAGGGATGTT
1 ATTTCATAGGGATGTT
3943 CTTGAAATTT
Statistics
Matches: 74, Mismatches: 24, Indels: 13
0.67 0.22 0.12
Matches are distributed among these distances:
20 2 0.03
21 1 0.01
22 55 0.74
23 14 0.19
24 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
ATTTCATAGGGATGTTAACAAA
Found at i:6055 original size:21 final size:22
Alignment explanation
Indices: 6021--6061 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6011 GACAAATTCG
*
6021 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
6043 TAACCCG-ATAACCCAAGAA
1 TAACCCGAATAACCCAAGAA
6062 TATTATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Done.