Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017418.1 Corchorus olitorius cultivar O-4 contig17451, 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: 42125
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:1776 original size:3 final size:3
Alignment explanation
Indices: 1768--1817 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1758 CAAGTGGCCC
*
1768 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1816 TC
1 TC
1818 CGGTCAGCCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:8223 original size:32 final size:30
Alignment explanation
Indices: 8180--8254 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 30
8170 CCTACATTAA
* *
8180 GGGCTAAATTGTCATCAATTTGGAAAGTTCATG
1 GGGC-AAATTGTCATAAATTT-GAAAATTCA-G
8213 GGGCAAATTGTCATAAATTTGAAAATTCAG
1 GGGCAAATTGTCATAAATTTGAAAATTCAG
*
8243 GGGTAAATTGTC
1 GGGCAAATTGTC
8255 GTGATTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 12 0.31
31 8 0.21
32 15 0.38
33 4 0.10
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (30 bp):
GGGCAAATTGTCATAAATTTGAAAATTCAG
Found at i:10038 original size:19 final size:20
Alignment explanation
Indices: 10008--10071 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
9998 TTGACACTGT
10008 TTAGCAATTGTACAGATGAGA
1 TTAGC-ATTGTACAGATGAGA
*
10029 TTA-CATTGTACAGATTAGA
1 TTAGCATTGTACAGATGAGA
* *
10048 TTAGGTACTGTACAGATGAGA
1 TTA-GCATTGTACAGATGAGA
10069 TTA
1 TTA
10072 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
TTAGCATTGTACAGATGAGA
Found at i:20963 original size:21 final size:19
Alignment explanation
Indices: 20929--21008 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 19
20919 TCTCATTAAA
20929 CTAAATAAAATCCACGTTGGC
1 CTAAA-AAAATCCACG-TGGC
* *
20950 CTAAAACAATTCCACCTGGC
1 CTAAAA-AAATCCACGTGGC
*
20970 CCAAAAAAATCCACGTGG-
1 CTAAAAAAATCCACGTGGC
*
20988 CTAAATTTAAATCCACGTGGC
1 CTAAA--AAAATCCACGTGGC
21009 TTAATTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.08
19 10 0.21
20 22 0.46
21 12 0.25
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (19 bp):
CTAAAAAAATCCACGTGGC
Found at i:20988 original size:19 final size:19
Alignment explanation
Indices: 20935--20988 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
20925 TAAACTAAAT
*
20935 AAAATCCACGTTGGCCTAAA
1 AAAATCCACG-TGGCCCAAA
* *
20955 ACAATTCCACCTGGCCCAAA
1 A-AAATCCACGTGGCCCAAA
20975 AAAATCCACGTGGC
1 AAAATCCACGTGGC
20989 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 11 0.39
20 10 0.36
21 7 0.25
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17
Consensus pattern (19 bp):
AAAATCCACGTGGCCCAAA
Found at i:21001 original size:20 final size:20
Alignment explanation
Indices: 20976--21018 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
20966 TGGCCCAAAA
20976 AAATCCACGTGGCTAAATTT
1 AAATCCACGTGGCTAAATTT
*
20996 AAATCCACGTGGCTTAATTT
1 AAATCCACGTGGCTAAATTT
21016 AAA
1 AAA
21019 GGGGTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATCCACGTGGCTAAATTT
Found at i:21261 original size:19 final size:19
Alignment explanation
Indices: 21237--21276 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
21227 TTTTCAACTT
21237 TTAGGCAATTTACCCCTCA
1 TTAGGCAATTTACCCCTCA
21256 TTAGGCAATTTACCCCTCA
1 TTAGGCAATTTACCCCTCA
21275 TT
1 TT
21277 GGACAGGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (19 bp):
TTAGGCAATTTACCCCTCA
Found at i:21380 original size:31 final size:31
Alignment explanation
Indices: 21328--21386 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
21318 AATTGATGGT
* *
21328 CAAAATAGCCATCTAACTTTGACAAAAAGGA
1 CAAAATAGCCATCTAAATTTGAAAAAAAGGA
*
21359 CAAAATAGCCCT-TAAAATTTGAAAAAAA
1 CAAAATAGCCATCT-AAATTTGAAAAAAA
21387 AACAAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (31 bp):
CAAAATAGCCATCTAAATTTGAAAAAAAGGA
Found at i:30993 original size:19 final size:18
Alignment explanation
Indices: 30960--30995 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30950 TGGAAATAAT
*
30960 TCTTCAATGATCTTCAAA
1 TCTTCAATCATCTTCAAA
30978 TCTTCAAATCATCTTCAA
1 TCTTC-AATCATCTTCAA
30996 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAATCATCTTCAAA
Found at i:31674 original size:30 final size:30
Alignment explanation
Indices: 31640--31711 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
31630 TTAATTAAAG
31640 TTGAAATTATTAAATAAAAAATAATAATTT
1 TTGAAATTATTAAATAAAAAATAATAATTT
* *
31670 TTGAAATTATTAAATGAATAATAATAATTT
1 TTGAAATTATTAAATAAAAAATAATAATTT
*
31700 TCGAAATTATTA
1 TTGAAATTATTA
31712 TTATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
TTGAAATTATTAAATAAAAAATAATAATTT
Found at i:32418 original size:8 final size:8
Alignment explanation
Indices: 32405--32432 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
32395 AGCAATGAAG
32405 GAAGCAAT
1 GAAGCAAT
32413 GAAGCAAT
1 GAAGCAAT
32421 GAAGCAAT
1 GAAGCAAT
32429 GAAG
1 GAAG
32433 GCATACTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.29, T:0.11
Consensus pattern (8 bp):
GAAGCAAT
Found at i:34810 original size:28 final size:28
Alignment explanation
Indices: 34770--34829 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
34760 CTCCTACGAA
34770 AGGGGAGGTAATCCTCCTCACATGCTCC
1 AGGGGAGGTAATCCTCCTCACATGCTCC
34798 AGGGGAGGTAATCCTCCTCACATGCTCC
1 AGGGGAGGTAATCCTCCTCACATGCTCC
34826 AGGG
1 AGGG
34830 TCCTCTGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (28 bp):
AGGGGAGGTAATCCTCCTCACATGCTCC
Found at i:36727 original size:17 final size:18
Alignment explanation
Indices: 36701--36741 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
36691 TAATTACAAT
*
36701 AATAAATAATTATAGT-A
1 AATAATTAATTATAGTCA
36718 AATAATTAATTATAGTCA
1 AATAATTAATTATAGTCA
36736 AATAAT
1 AATAAT
36742 AAAATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (18 bp):
AATAATTAATTATAGTCA
Found at i:37134 original size:19 final size:19
Alignment explanation
Indices: 37110--37148 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
37100 CATGATGTTC
37110 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
37129 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
37148 T
1 T
37149 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Done.