Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023764.1 Corchorus olitorius cultivar O-4 contig23797, 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: 51065
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Found at i:1190 original size:7 final size:7
Alignment explanation
Indices: 1178--1221 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
1168 TACGACATAT
1178 ATACTAA
1 ATACTAA
1185 ATACTAA
1 ATACTAA
1192 ATACT-A
1 ATACTAA
1198 ATACTAA
1 ATACTAA
1205 ATACTAA
1 ATACTAA
1212 ATACTAA
1 ATACTAA
1219 ATA
1 ATA
1222 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (7 bp):
ATACTAA
Found at i:1203 original size:20 final size:20
Alignment explanation
Indices: 1178--1218 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1168 TACGACATAT
1178 ATACTAAATACTAAATACTA
1 ATACTAAATACTAAATACTA
1198 ATACTAAATACTAAATACTA
1 ATACTAAATACTAAATACTA
1218 A
1 A
1219 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (20 bp):
ATACTAAATACTAAATACTA
Found at i:1242 original size:27 final size:28
Alignment explanation
Indices: 1174--1249 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
1164 TTTTTACGAC
1174 ATATATACTAAATACTAAATACTAATACT
1 ATATATACTAAATACTAAATA-TAATACT
1203 A-A-ATACTAAATACTAAATATATATA-T
1 ATATATACTAAATACTAAATATA-ATACT
*
1229 ATATATA-TATATACTAAATAT
1 ATATATACTAAATACTAAATAT
1250 TATTTGAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 4 0.09
27 34 0.79
28 4 0.09
29 1 0.02
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (28 bp):
ATATATACTAAATACTAAATATAATACT
Found at i:3170 original size:24 final size:24
Alignment explanation
Indices: 3112--3227 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
3102 CTTGGTTGAT
* *
3112 GGTGCCGGTGCATCATCAGCAGGGC
1 GGTGCCGGTGCATCATCGGC-TGGC
3137 GGTGCCGGTGCATCATCGGCTGGC
1 GGTGCCGGTGCATCATCGGCTGGC
*
3161 GGTGCTGGTGCATCATCGGCTGGC
1 GGTGCCGGTGCATCATCGGCTGGC
* *
3185 GGTGCTGGTGCATCATCGGCTGGT
1 GGTGCCGGTGCATCATCGGCTGGC
*
3209 GGTGCCGGTGCAGCATCGG
1 GGTGCCGGTGCATCATCGG
3228 ATGAACAATG
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
24 66 0.78
25 19 0.22
ACGTcount: A:0.10, C:0.26, G:0.42, T:0.22
Consensus pattern (24 bp):
GGTGCCGGTGCATCATCGGCTGGC
Found at i:13068 original size:32 final size:32
Alignment explanation
Indices: 13031--13110 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
13021 CTTCTCCACT
*
13031 AAAACTAAAGTAATAATATTTCACCCCAAAAA
1 AAAACTAAAGTAATAATATTTCACCCAAAAAA
*
13063 AAAACTAAAGCAATAATATTTCACCCAAAAAA
1 AAAACTAAAGTAATAATATTTCACCCAAAAAA
13095 AAAACTAAAGTAATAA
1 AAAACTAAAGTAATAA
13111 AAAAAATACT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.60, C:0.16, G:0.04, T:0.20
Consensus pattern (32 bp):
AAAACTAAAGTAATAATATTTCACCCAAAAAA
Found at i:25308 original size:12 final size:12
Alignment explanation
Indices: 25284--25317 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
25274 GATTTTGACT
25284 TTTAGTATTTGGA
1 TTTAGT-TTTGGA
25297 TTTAGTTTTGGA
1 TTTAGTTTTGGA
25309 TTTGAGTTT
1 TTT-AGTTT
25318 CTGCTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
TTTAGTTTTGGA
Found at i:35187 original size:51 final size:51
Alignment explanation
Indices: 35087--35187 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
35077 GTTCATCAAA
* **
35087 TTCTCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
35138 TTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
35188 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
50 2 0.05
51 40 0.93
52 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (51 bp):
TTCTCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:40834 original size:11 final size:11
Alignment explanation
Indices: 40793--40834 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
40783 AATGATAAAT
*
40793 ATAAATTATAT
1 ATAAATTATAA
40804 ATAAATTAT-A
1 ATAAATTATAA
40814 AT-AA-TATAA
1 ATAAATTATAA
40823 ATAAATTATAA
1 ATAAATTATAA
40834 A
1 A
40835 AACAAATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 3 0.11
9 5 0.19
10 4 0.15
11 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAAATTATAA
Done.