Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024633.1 Corchorus olitorius cultivar O-4 contig24666, 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: 28648
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:97 original size:23 final size:22
Alignment explanation
Indices: 62--107 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
52 CCAAATTCGG
*
62 GTCCAGTCGTCAAACCCGCGCGC
1 GTCCAGGCGTC-AACCCGCGCGC
*
85 GTCCAGGCTTCAACCCGCGCGC
1 GTCCAGGCGTCAACCCGCGCGC
107 G
1 G
108 GCTAGTGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.15, C:0.43, G:0.28, T:0.13
Consensus pattern (22 bp):
GTCCAGGCGTCAACCCGCGCGC
Found at i:13992 original size:29 final size:29
Alignment explanation
Indices: 13951--14019 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
13941 CTATCTTTCA
*
13951 ATTG-TTGATTTGAAGTGCTA-TATTTTGCT
1 ATTGATTGA-TTGAAGTGCAATTA-TTTGCT
* *
13980 ATTGATTGATTGAATTGCAATTATTTGTT
1 ATTGATTGATTGAAGTGCAATTATTTGCT
14009 AGTTGATTGAT
1 A-TTGATTGAT
14020 AGATTGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (29 bp):
ATTGATTGATTGAAGTGCAATTATTTGCT
Found at i:19665 original size:10 final size:9
Alignment explanation
Indices: 19633--19694 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 9
19623 TTATATAGTA
19633 GTAAGATA-
1 GTAAGATAT
19641 GTAAGATAT
1 GTAAGATAT
19650 -TAAGATAGT
1 GTAAGATA-T
19659 GTAAGATAT
1 GTAAGATAT
19668 AGTAAGATA-
1 -GTAAGATAT
*
19677 GTAAGATAA
1 GTAAGATAT
19686 GATAAGATA
1 G-TAAGATA
19695 AGATAAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
8 23 0.48
9 3 0.06
10 22 0.46
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (9 bp):
GTAAGATAT
Found at i:19680 original size:18 final size:18
Alignment explanation
Indices: 19631--19694 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
19621 TTTTATATAG
19631 TAGTAAGATAGTAAGATA
1 TAGTAAGATAGTAAGATA
19649 T--TAAGATAGTGTAAGATA
1 TAGTAAGATA--GTAAGATA
19667 TAGTAAGATAGTAAGATA
1 TAGTAAGATAGTAAGATA
19685 -AGATAAGATA
1 TAG-TAAGATA
19695 AGATAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.17
17 2 0.05
18 25 0.61
20 7 0.17
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (18 bp):
TAGTAAGATAGTAAGATA
Found at i:19688 original size:5 final size:5
Alignment explanation
Indices: 19660--19700 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
19650 TAAGATAGTG
19660 TAAGA TATAG- TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA TAA
1 TAAGA TA-AGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAA
19701 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 1 0.03
4 6 0.19
5 23 0.72
6 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:19691 original size:28 final size:28
Alignment explanation
Indices: 19638--19694 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
19628 TAGTAGTAAG
* *
19638 ATAGTAAGATATTAAGATAGTGTAAGAT
1 ATAGTAAGATAGTAAGATAGTATAAGAT
19666 ATAGTAAGATAGTAAGATAAG-ATAAGAT
1 ATAGTAAGATAGTAAGAT-AGTATAAGAT
19694 A
1 A
19695 AGATAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (28 bp):
ATAGTAAGATAGTAAGATAGTATAAGAT
Found at i:22368 original size:13 final size:13
Alignment explanation
Indices: 22350--22380 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
22340 CAAAACCCGT
22350 TGGAAATTGTAAG
1 TGGAAATTGTAAG
22363 TGGAAATTGTAAG
1 TGGAAATTGTAAG
22376 TGGAA
1 TGGAA
22381 GTTGATCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (13 bp):
TGGAAATTGTAAG
Found at i:24404 original size:21 final size:22
Alignment explanation
Indices: 24380--24421 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
24370 GTGACACTGC
* *
24380 CCACCTGGGTTCTCAA-GCAAA
1 CCACATGGGTGCTCAACGCAAA
24401 CCACATGGGTGCTCAACGCAA
1 CCACATGGGTGCTCAACGCAA
24422 CCATGTGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (22 bp):
CCACATGGGTGCTCAACGCAAA
Found at i:25734 original size:26 final size:26
Alignment explanation
Indices: 25708--25757 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
25698 CTCAAACTAT
*
25708 TTTC-TTGATCTTTAGTTTTATTTTA
1 TTTCATTGATCTTTAGTTTAATTTTA
* *
25733 TTTCATTGGTTTTTAGTTTAATTTT
1 TTTCATTGATCTTTAGTTTAATTTT
25758 CTATTTCGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.16, C:0.06, G:0.10, T:0.68
Consensus pattern (26 bp):
TTTCATTGATCTTTAGTTTAATTTTA
Found at i:26036 original size:11 final size:11
Alignment explanation
Indices: 26022--26055 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
26012 TTTTCATTAT
26022 TTTTATTTTTC
1 TTTTATTTTTC
26033 TTTTATTTTT-
1 TTTTATTTTTC
*
26043 GTTTATTTTTC
1 TTTTATTTTTC
26054 TT
1 TT
26056 AGTTACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:26036 original size:21 final size:21
Alignment explanation
Indices: 26012--26055 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26002 TTATCTTCTT
26012 TTTTCATTATT-TTTATTTTTC
1 TTTT-ATTATTGTTTATTTTTC
*
26033 TTTTATTTTTGTTTATTTTTC
1 TTTTATTATTGTTTATTTTTC
26054 TT
1 TT
26056 AGTTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTATTATTGTTTATTTTTC
Found at i:28226 original size:15 final size:15
Alignment explanation
Indices: 28196--28237 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
28186 TTACTCTGCT
28196 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
28212 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
28227 TTGCTTTCTGT
1 TTGTTTTCTGT
28238 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.