Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016334.1 Corchorus olitorius cultivar O-4 contig16367, 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: 33490
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1206 original size:15 final size:15
Alignment explanation
Indices: 1186--1214 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1176 TGATGTTTTG
1186 AGTCAGTTGAGTTTA
1 AGTCAGTTGAGTTTA
1201 AGTCAGTTGAGTTT
1 AGTCAGTTGAGTTT
1215 GTTTAGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (15 bp):
AGTCAGTTGAGTTTA
Found at i:1516 original size:21 final size:23
Alignment explanation
Indices: 1492--1535 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
1482 CATGTCCAAT
1492 TTATTGTAATTT-A-TTTTATAA
1 TTATTGTAATTTCATTTTTATAA
1513 TTATTGTAATTTCATTTTTATAA
1 TTATTGTAATTTCATTTTTATAA
1536 ATGAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.57
22 1 0.05
23 8 0.38
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTATTGTAATTTCATTTTTATAA
Found at i:3563 original size:5 final size:5
Alignment explanation
Indices: 3549--3583 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
3539 TCAAGTAATT
*
3549 AAAGG AAAGG GAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
3584 GGAGGGAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:4493 original size:2 final size:2
Alignment explanation
Indices: 4488--4530 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4478 ACTAAAAATA
*
4488 AT AT AT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4529 AT
1 AT
4531 CCTTCAGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5113 original size:13 final size:13
Alignment explanation
Indices: 5095--5120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5085 ATAGTAGTGA
5095 GAACATCTAGCAG
1 GAACATCTAGCAG
5108 GAACATCTAGCAG
1 GAACATCTAGCAG
5121 CATGCCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
GAACATCTAGCAG
Found at i:5253 original size:65 final size:64
Alignment explanation
Indices: 5142--5272 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 64
5132 TATACTTCCC
*
5142 AAAAAACCAAAACTTAATCAAGGGGGACAGGGAAATCCGTCCTTGTTCAAAATGAAAAAAAAAA
1 AAAAAACCAAAACTTAATCAAGGGGGACAGGGAAATCCATCCTTGTTCAAAATGAAAAAAAAAA
* * ** *
5206 AAAAAACCAAAAACTTGATCAAGGGGGACAGGGAAGTCCATTTTTGTTCAAAATGAAAACAAAAA
1 AAAAAACC-AAAACTTAATCAAGGGGGACAGGGAAATCCATCCTTGTTCAAAATGAAAAAAAAAA
5271 AA
1 AA
5273 GATGAAGGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 8 0.13
65 52 0.87
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.17
Consensus pattern (64 bp):
AAAAAACCAAAACTTAATCAAGGGGGACAGGGAAATCCATCCTTGTTCAAAATGAAAAAAAAAA
Found at i:6131 original size:20 final size:20
Alignment explanation
Indices: 6106--6143 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6096 TAATTTCATT
6106 TAATTAATTTAA-TATTTTTA
1 TAATTAA-TTAATTATTTTTA
6126 TAATTAATTAATTATTTT
1 TAATTAATTAATTATTTT
6144 ATTTTTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTAATTAATTATTTTTA
Found at i:7729 original size:17 final size:17
Alignment explanation
Indices: 7707--7739 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7697 GTAATTTCAT
7707 TGGGTGTTTCAAATAAA
1 TGGGTGTTTCAAATAAA
7724 TGGGTGTTTCAAATAA
1 TGGGTGTTTCAAATAA
7740 TATTTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
TGGGTGTTTCAAATAAA
Found at i:26101 original size:48 final size:48
Alignment explanation
Indices: 26048--26143 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
26038 TCCCTAGAAG
26048 ACACATGTCACCCTTCAGGAGCCGCTTGTGTAGTCTGCTAAACTCCAC
1 ACACATGTCACCCTTCAGGAGCCGCTTGTGTAGTCTGCTAAACTCCAC
*
26096 ACACATGTCACCTTTCAGGAGCCGCTTGTGTAGTCTGCTAAACTCCAC
1 ACACATGTCACCCTTCAGGAGCCGCTTGTGTAGTCTGCTAAACTCCAC
26144 CGCCGGTGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (48 bp):
ACACATGTCACCCTTCAGGAGCCGCTTGTGTAGTCTGCTAAACTCCAC
Found at i:32961 original size:8 final size:9
Alignment explanation
Indices: 32950--32991 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
32940 ATTAAAAAAT
32950 TATTAT-TA
1 TATTATATA
32958 TATTATATTA
1 TATTATA-TA
32968 TATTATATA
1 TATTATATA
32977 TATATATATA
1 TAT-TATATA
32987 TATTA
1 TATTA
32992 AAAAGTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 6 0.19
9 7 0.23
10 18 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTATATA
Found at i:33151 original size:224 final size:224
Alignment explanation
Indices: 32756--33185 Score: 774
Period size: 224 Copynumber: 1.9 Consensus size: 224
32746 CACATCTATC
* *
32756 TATACTATATTAAAAAGTACATACTCCTGTAAAAATTTTGAATTGCCCATTATACCCTTATTTTT
1 TATACTATATTAAAAAGTACATACTCCTGTAAAAATTTTGAATCGCCCAGTATACCCTTATTTTT
32821 CGAATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTT
66 CGAATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTT
*
32886 TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCACTATTATAATT-AAAAAAT
131 TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCACTATCATAATTAAAAAAAT
32950 TATTATTATATTATATTATATTATATATATA
196 TA-TA-TATATTATATTATATTATATATATA
* *
32981 TATA-TATATTAAAAAGTACATACTCTTGTAAAACTTTTGAATCGCCCAGTATACCCTTATTTTT
1 TATACTATATTAAAAAGTACATACTCCTGTAAAAATTTTGAATCGCCCAGTATACCCTTATTTTT
*
33045 CGAATATATTTCTTAAATGCCATTGTTTAGATTTTTATAGTTTTACTCAACTAAAAACTCTATTT
66 CGAATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTT
33110 TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCACTATCATAATTAAAAAAAT
131 TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCACTATCATAATTAAAAAAAT
33175 TATATATATTA
196 TATATATATTA
33186 GAATTTTTTA
Statistics
Matches: 198, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
223 7 0.04
224 178 0.90
225 13 0.07
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (224 bp):
TATACTATATTAAAAAGTACATACTCCTGTAAAAATTTTGAATCGCCCAGTATACCCTTATTTTT
CGAATATATTTCTTAAATGCCATTGTTTAGACTTTTATAGTTTTACTCAACTAAAAACTCTATTT
TTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCACTATCATAATTAAAAAAAT
TATATATATTATATTATATTATATATATA
Done.