Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011954.1 Corchorus olitorius cultivar O-4 contig11987, 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: 33444
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8414 original size:36 final size:36
Alignment explanation
Indices: 8373--8446 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
8363 ATAATGTCCA
8373 TAGCCTCTCTACTATCAATATGTTAATGTTGCTTTT
1 TAGCCTCTCTACTATCAATATGTTAATGTTGCTTTT
8409 TAGCCTCTCTACTATCAATATGTTAATGTTGCTTTT
1 TAGCCTCTCTACTATCAATATGTTAATGTTGCTTTT
8445 TA
1 TA
8447 TTGATAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (36 bp):
TAGCCTCTCTACTATCAATATGTTAATGTTGCTTTT
Found at i:10458 original size:25 final size:25
Alignment explanation
Indices: 10413--10464 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
10403 TTTTGAACTC
* *
10413 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATAATT
*
10438 ATTATTTATT-TAATAATATATAATT
1 ATTATTTATTAT-ATAAAATATAATT
10463 AT
1 AT
10465 ATCTAAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATAATT
Found at i:10463 original size:22 final size:22
Alignment explanation
Indices: 10381--10464 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 22
10371 CGTTTAGTAA
*
10381 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTAATTATTTA-T
* * * *
10405 TTGAACT-CATTATTTA-TTAT
1 TTAAAATATATTAATTATTTAT
*
10425 TTAAAATATATTTATTATTTAT
1 TTAAAATATATTAATTATTTAT
10447 TTAATAATATA-TAATTAT
1 TTAA-AATATATTAATTAT
10465 ATCTAAGATA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
20 6 0.12
21 9 0.19
22 22 0.46
23 7 0.15
24 4 0.08
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (22 bp):
TTAAAATATATTAATTATTTAT
Found at i:12468 original size:17 final size:18
Alignment explanation
Indices: 12448--12481 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12438 AAAAGTAAGA
12448 AAATG-TTAAAATTTTTG
1 AAATGTTTAAAATTTTTG
*
12465 AAATGTTTATAATTTTT
1 AAATGTTTAAAATTTTT
12482 TTTACTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AAATGTTTAAAATTTTTG
Found at i:13559 original size:18 final size:19
Alignment explanation
Indices: 13520--13559 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
13510 ATGCTCTCAT
13520 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
13541 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
13559 T
1 T
13560 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:16238 original size:42 final size:42
Alignment explanation
Indices: 16166--16256 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
16156 AGTGCATTAC
*
16166 CTAA-ATTCTACTTCATCTCTAAGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAAGTAATTCATCAAAATAAAG
*
16207 CTAATATTCTACTCCATCTCT-AGATACTTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAAG-TAATTCATCAAAATAAAG
16249 CTAATATT
1 CTAATATT
16257 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 6 0.13
42 40 0.87
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTCTAAGTAATTCATCAAAATAAAG
Found at i:17201 original size:2 final size:2
Alignment explanation
Indices: 17188--17224 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
17178 ACTAAAAATA
17188 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17225 GATAGTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18635 original size:61 final size:60
Alignment explanation
Indices: 18566--18706 Score: 201
Period size: 61 Copynumber: 2.3 Consensus size: 60
18556 AATGTTTGTC
* * * *
18566 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCTTAATATTATCG
1 AAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGACCAAATAAGGGCCTAACATTATCG
** *
18626 AAAAATGCTCAAATAAGGGTTCAATCTTTTAATTTGACCAAATAAGGGCCTAACGTTATCG
1 -AAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGACCAAATAAGGGCCTAACATTATCG
*
18687 AAAATGCTCAAAAAAGGGCC
1 AAAATGCTCAAATAAGGGCC
18707 TGGCGTCAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
60 17 0.24
61 53 0.76
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGACCAAATAAGGGCCTAACATTATCG
Found at i:25132 original size:15 final size:15
Alignment explanation
Indices: 25112--25141 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25102 GGACTCATCC
25112 AATGAAGAAAATGGT
1 AATGAAGAAAATGGT
25127 AATGAAGAAAATGGT
1 AATGAAGAAAATGGT
25142 GATGGTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (15 bp):
AATGAAGAAAATGGT
Found at i:26128 original size:66 final size:66
Alignment explanation
Indices: 26035--26167 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
26025 ACTTATTTAT
*
26035 AATTGAGAAGTTTCTTTTATTTATTTGGCAGCTAGATGATTTGGTTTTGTGTAGGATTTACAAGA
1 AATTGAGAAGTTTCTTTTATTTATTTGGCAGCTAGATGATTGGGTTTTGTGTAGGATTTACAAGA
26100 A
66 A
26101 AATTGAGAAGTTTCTTTTATTTATTTGGCAGCTAGATGATTGGGTTTTGTGTAGGATTTACAAGA
1 AATTGAGAAGTTTCTTTTATTTATTTGGCAGCTAGATGATTGGGTTTTGTGTAGGATTTACAAGA
26166 A
66 A
26167 A
1 A
26168 GATGAAAAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (66 bp):
AATTGAGAAGTTTCTTTTATTTATTTGGCAGCTAGATGATTGGGTTTTGTGTAGGATTTACAAGA
A
Found at i:26737 original size:19 final size:19
Alignment explanation
Indices: 26713--26754 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
26703 TTGGCAGCAA
26713 CTTTGGACTTTATTATTAC
1 CTTTGGACTTTATTATTAC
*
26732 CTTTGGAGTTTATTATTAC
1 CTTTGGACTTTATTATTAC
26751 CTTT
1 CTTT
26755 TTGCTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.55
Consensus pattern (19 bp):
CTTTGGACTTTATTATTAC
Done.