Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017839.1 Corchorus olitorius cultivar O-4 contig17872, 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: 26200
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:1194 original size:27 final size:27
Alignment explanation
Indices: 1164--1254 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
1154 TGGCTAATTT
1164 GAAAATTTCATCTAATCCTTTATTAAA
1 GAAAATTTCATCTAATCCTTTATTAAA
* * * * * *
1191 GAAAAGATT-ATTTATTGACATTGTTATAGA
1 GAAAA-TTTCATCTAAT-CCTTTATTA-A-A
1221 TGGAAAATTTCATCTAATCCTTTATTAAA
1 --GAAAATTTCATCTAATCCTTTATTAAA
1250 GAAAA
1 GAAAA
1255 GATTATTTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
27 15 0.33
28 8 0.18
29 2 0.04
30 2 0.04
31 8 0.18
32 10 0.22
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (27 bp):
GAAAATTTCATCTAATCCTTTATTAAA
Found at i:1227 original size:59 final size:59
Alignment explanation
Indices: 1164--1286 Score: 246
Period size: 59 Copynumber: 2.1 Consensus size: 59
1154 TGGCTAATTT
1164 GAAAATTTCATCTAATCCTTTATTAAAGAAAAGATTATTTATTGACATTGTTATAGATG
1 GAAAATTTCATCTAATCCTTTATTAAAGAAAAGATTATTTATTGACATTGTTATAGATG
1223 GAAAATTTCATCTAATCCTTTATTAAAGAAAAGATTATTTATTGACATTGTTATAGATG
1 GAAAATTTCATCTAATCCTTTATTAAAGAAAAGATTATTTATTGACATTGTTATAGATG
1282 GAAAA
1 GAAAA
1287 CCAGCTGGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (59 bp):
GAAAATTTCATCTAATCCTTTATTAAAGAAAAGATTATTTATTGACATTGTTATAGATG
Found at i:6692 original size:3 final size:3
Alignment explanation
Indices: 6686--6737 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
6676 GGAGGAGGAA
* * ** *
6686 GTG GTG GTG GTG GTG GAG GTG GAG GTG GCA GTG GGG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
6734 GTG G
1 GTG G
6738 AGGAGGTGGC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.06, C:0.02, G:0.67, T:0.25
Consensus pattern (3 bp):
GTG
Found at i:6706 original size:12 final size:12
Alignment explanation
Indices: 6686--6746 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
6676 GGAGGAGGAA
*
6686 GTGGTGGTGGTG
1 GTGGAGGTGGTG
*
6698 GTGGAGGTGGAG
1 GTGGAGGTGGTG
*
6710 GTGGCA-GTGGGG
1 GTGG-AGGTGGTG
*
6722 GTGGTGGTGGTG
1 GTGGAGGTGGTG
*
6734 GTGGAGGAGGTG
1 GTGGAGGTGGTG
6746 G
1 G
6747 CAGTGGCGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 39 0.98
13 1 0.03
ACGTcount: A:0.08, C:0.02, G:0.67, T:0.23
Consensus pattern (12 bp):
GTGGAGGTGGTG
Found at i:6710 original size:30 final size:30
Alignment explanation
Indices: 6676--6777 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 30
6666 TGGTGGGAAA
6676 GGAGGAGGAAGTGGTGGTGGTGGTGGAGGT
1 GGAGGAGGAAGTGGTGGTGGTGGTGGAGGT
* * * *
6706 GGAGGTGGCAGTGGGGGTGGTGGTGGTGGT
1 GGAGGAGGAAGTGGTGGTGGTGGTGGAGGT
** * *
6736 GGAGGA-G--GTGGCAGTGGCGGTGGCGGT
1 GGAGGAGGAAGTGGTGGTGGTGGTGGAGGT
6763 GGAGGAGGAAGTGGT
1 GGAGGAGGAAGTGGT
6778 CAAGGTAACG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 22 0.37
28 1 0.02
29 1 0.02
30 35 0.59
ACGTcount: A:0.14, C:0.04, G:0.64, T:0.19
Consensus pattern (30 bp):
GGAGGAGGAAGTGGTGGTGGTGGTGGAGGT
Found at i:6730 original size:33 final size:33
Alignment explanation
Indices: 6688--6771 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
6678 AGGAGGAAGT
* *
6688 GGTGGTGGTGGTGGAGGTGGAGGTGGCAGTGGG
1 GGTGGTGGTGGTGGAGGAGGAGGTGGCAGTGGC
*
6721 GGTGGTGGTGGTGGTGGAGGAGGTGGCAGTGGC
1 GGTGGTGGTGGTGGAGGAGGAGGTGGCAGTGGC
* *
6754 GGTGGCGGTGGAGGAGGA
1 GGTGGTGGTGGTGGAGGA
6772 AGTGGTCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.11, C:0.05, G:0.65, T:0.19
Consensus pattern (33 bp):
GGTGGTGGTGGTGGAGGAGGAGGTGGCAGTGGC
Found at i:6757 original size:12 final size:12
Alignment explanation
Indices: 6704--6767 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
6694 GGTGGTGGAG
6704 GTGGAGGTGGCA
1 GTGGAGGTGGCA
* **
6716 GTGGGGGTGGTG
1 GTGGAGGTGGCA
*
6728 GTGGTGGTGG-A
1 GTGGAGGTGGCA
6739 --GGAGGTGGCA
1 GTGGAGGTGGCA
* *
6749 GTGGCGGTGGCG
1 GTGGAGGTGGCA
6761 GTGGAGG
1 GTGGAGG
6768 AGGAAGTGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
9 7 0.17
10 1 0.03
12 32 0.80
ACGTcount: A:0.09, C:0.06, G:0.66, T:0.19
Consensus pattern (12 bp):
GTGGAGGTGGCA
Found at i:6763 original size:18 final size:18
Alignment explanation
Indices: 6698--6764 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 18
6688 GGTGGTGGTG
6698 GTGGAGGTGGAGGTGGCA
1 GTGGAGGTGGAGGTGGCA
* *
6716 GTGGGGGTGGTGGT-G--
1 GTGGAGGTGGAGGTGGCA
* *
6731 GTGGTGGAGGAGGTGGCA
1 GTGGAGGTGGAGGTGGCA
* *
6749 GTGGCGGTGGCGGTGG
1 GTGGAGGTGGAGGTGG
6765 AGGAGGAAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
17 1 0.03
18 25 0.66
ACGTcount: A:0.09, C:0.06, G:0.66, T:0.19
Consensus pattern (18 bp):
GTGGAGGTGGAGGTGGCA
Found at i:7040 original size:114 final size:116
Alignment explanation
Indices: 6810--7109 Score: 451
Period size: 114 Copynumber: 2.6 Consensus size: 116
6800 GTGGAGGGGG
* * * *
6810 TGGTGGTGGGGGTGGCAGTGGTAGTGGTGGAGGGAAAGGTAATCCACACAAGAAGGGAAAAGGAA
1 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
6875 GTGGAGGTGGAGGTGGAGGCGGAGGAGGAAGTGGTCAGGGTAACGGAGGGGGAAA
66 GTGGA----GAGGTGGAGGCGGAGGAGGAAGTGGTCAGGGTAACGGAGGGGGAAA
* *
6930 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGTGGCAAAGGTAATCCACACAAGAAAGGAAAAGGAA
1 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
* * *
6995 GTGGA-A-GTGGAGGTGGAGGAGGAAGTGGTCAGGGTAATGGTGGGGGAAA
66 GTGGAGAGGTGGAGGCGGAGGAGGAAGTGGTCAGGGTAACGGAGGGGGAAA
* *
7044 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAACCCACACAAGAAAAGAAAAGGAA
1 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
7109 G
66 G
7110 GGGCAATGGC
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
114 102 0.61
115 1 0.01
120 65 0.39
ACGTcount: A:0.31, C:0.07, G:0.48, T:0.14
Consensus pattern (116 bp):
TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
GTGGAGAGGTGGAGGCGGAGGAGGAAGTGGTCAGGGTAACGGAGGGGGAAA
Found at i:7151 original size:114 final size:112
Alignment explanation
Indices: 6810--7151 Score: 348
Period size: 114 Copynumber: 2.9 Consensus size: 112
6800 GTGGAGGGGG
* * * *
6810 TGGTGGTGGGGGTGGCAGTGGTAGTGGTGGAGGGAAAGGTAATCCACACAAGAAGGGAAAAGGAA
1 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
* * * * * *
6875 GTGGAGGTGGAGGTGGAGGCGGAGGAGGAAGTGGTCAGGGTAACGGAGGGGGAAA
66 GTGGA-ATGGA-GTGGTGGAGGAGGAGGAGGCGG-C--GG---CGGTGGGGGAAA
* *
6930 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGTGGCAAAGGTAATCCACACAAGAAAGGAAAAGGAA
1 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
* * **
6995 GTGGAAGTGGA--GGTGGAGGAGGAAGTGGTCAGG-GTAATGGTGGGGGAAA
66 GTGGAA-TGGAGTGGTGGAGGAGGAGGAGG-C-GGCG--GCGGTGGGGGAAA
* *
7044 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAACCCACACAAGAAAAGAAAAGGAA
1 TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
* *
7109 GGGGCAATGGCAGTGGTGGAGGAGGAGGCGGCGGCGGCGGTGG
66 GTGG-AATGG-AGTGGTGGAGGAGGAGGAGGCGGCGGCGGTGG
7152 CGGTGGGGGA
Statistics
Matches: 188, Mismatches: 24, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
114 82 0.44
115 6 0.03
116 2 0.01
117 27 0.14
119 2 0.01
120 69 0.37
ACGTcount: A:0.29, C:0.08, G:0.49, T:0.13
Consensus pattern (112 bp):
TGGTGGAGGGGGTGGCAGTGGTAATGGTGGAGGAAAAGGTAATCCACACAAGAAAGGAAAAGGAA
GTGGAATGGAGTGGTGGAGGAGGAGGAGGCGGCGGCGGTGGGGGAAA
Found at i:7171 original size:21 final size:21
Alignment explanation
Indices: 7132--7182 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
7122 TGGTGGAGGA
* * *
7132 GGAGGCGGCGGCGGCGGTGGC
1 GGAGGGGGAGGCGGAGGTGGC
* *
7153 GGTGGGGGAGGCGGAGGTGGT
1 GGAGGGGGAGGCGGAGGTGGC
7174 GGAGGGGGA
1 GGAGGGGGA
7183 AATGGCCAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.71, T:0.08
Consensus pattern (21 bp):
GGAGGGGGAGGCGGAGGTGGC
Found at i:7241 original size:33 final size:33
Alignment explanation
Indices: 7204--7274 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
7194 TCACGGATGG
*
7204 GGTGG-AGGAAGTGGAGGGGGAGGAGGTGGGGGA
1 GGTGGCAGGAA-TGGAGGAGGAGGAGGTGGGGGA
* * *
7237 GGTGGCGGGAATGGTGGAGGAGGAGGTGGTGGA
1 GGTGGCAGGAATGGAGGAGGAGGAGGTGGGGGA
7270 GGTGG
1 GGTGG
7275 TGGCGGCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.18, C:0.01, G:0.68, T:0.13
Consensus pattern (33 bp):
GGTGGCAGGAATGGAGGAGGAGGAGGTGGGGGA
Found at i:7286 original size:33 final size:33
Alignment explanation
Indices: 7222--7310 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 33
7212 AAGTGGAGGG
* * *
7222 GGAGGAGGTGGGGGAGGTGGCGGGAATGGTGGA
1 GGAGGAGGTGGAGGAGGTGGTGGGAACGGTGGA
* * *
7255 GGAGGAGGTGGTGGAGGTGGTGGCG-GCGGTGGT
1 GGAGGAGGTGGAGGAGGTGGTGG-GAACGGTGGA
* * *
7288 GGTGGAGGAGGAGGAGGGGGTGG
1 GGAGGAGGTGGAGGAGGTGGTGG
7311 TCAAGGTGGA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.69, T:0.13
Consensus pattern (33 bp):
GGAGGAGGTGGAGGAGGTGGTGGGAACGGTGGA
Found at i:10738 original size:16 final size:18
Alignment explanation
Indices: 10702--10738 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
10692 AATTGCTCCG
*
10702 AAAACAACCCAATTCCAT
1 AAAACAACCAAATTCCAT
10720 AAAA-AACCAAATTCC-T
1 AAAACAACCAAATTCCAT
10736 AAA
1 AAA
10739 TATAACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 10 0.56
18 4 0.22
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAACAACCAAATTCCAT
Done.