Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020778.1 Corchorus olitorius cultivar O-4 contig20811, 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: 4579
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:135 original size:18 final size:18
Alignment explanation
Indices: 114--156 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
104 TGAAAAAACA
*
114 GAAAAATCAAAAAAAAAT
1 GAAAAAACAAAAAAAAAT
* *
132 GAAAAAAGAAGAAAAAAT
1 GAAAAAACAAAAAAAAAT
150 GAAAAAA
1 GAAAAAA
157 AAAGTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (18 bp):
GAAAAAACAAAAAAAAAT
Found at i:144 original size:28 final size:28
Alignment explanation
Indices: 104--159 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
94 ATTTTTTTTC
*
104 TGAAAAAACAG-AAAAATCAAAAAAAAA
1 TGAAAAAAAAGAAAAAATCAAAAAAAAA
*
131 TGAAAAAAGAAGAAAAAATGAAAAAAAAA
1 TGAAAAAA-AAGAAAAAATCAAAAAAAAA
160 GTTTCTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 15 0.60
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.07
Consensus pattern (28 bp):
TGAAAAAAAAGAAAAAATCAAAAAAAAA
Found at i:1212 original size:17 final size:17
Alignment explanation
Indices: 1190--1247 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
1180 TTTTAAGAAA
1190 AATATTAAATAATATAT
1 AATATTAAATAATATAT
1207 AATATTAAATAATA-A-
1 AATATTAAATAATATAT
1222 AAT-TT---T-ATATAT
1 AATATTAAATAATATAT
1234 AATATTAAATAATA
1 AATATTAAATAATA
1248 AAATTTTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
10 3 0.09
11 2 0.06
12 3 0.09
13 2 0.06
14 2 0.06
15 3 0.09
16 2 0.06
17 17 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATTAAATAATATAT
Found at i:1231 original size:27 final size:27
Alignment explanation
Indices: 1201--1256 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1191 ATATTAAATA
1201 ATATATAATATTAAATAATAAAATTTT
1 ATATATAATATTAAATAATAAAATTTT
1228 ATATATAATATTAAATAATAAAATTTT
1 ATATATAATATTAAATAATAAAATTTT
1255 AT
1 AT
1257 CTAAGGTCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATAATATTAAATAATAAAATTTT
Found at i:3051 original size:28 final size:29
Alignment explanation
Indices: 3020--3076 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
3010 AAAAAACCCT
*
3020 AAAATGCATTACAGAAAA-CCTCAAGTCC
1 AAAATCCATTACAGAAAACCCTCAAGTCC
*
3048 AAAATCCATTACAGAAAACCCTGAAGTCC
1 AAAATCCATTACAGAAAACCCTCAAGTCC
3077 GAGTAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.18
Consensus pattern (29 bp):
AAAATCCATTACAGAAAACCCTCAAGTCC
Found at i:3377 original size:344 final size:344
Alignment explanation
Indices: 2750--3438 Score: 1351
Period size: 344 Copynumber: 2.0 Consensus size: 344
2740 GACTGTGTAG
2750 AAATATCAAAGGGACACATGAGCATAAAATTGAAATGTTTGAAGACTATTTCATAAATAACCCCT
1 AAATATCAAAGGGACACATGAGCATAAAATTGAAATGTTTGAAGACTATTTCATAAATAACCCCT
* *
2815 TTTTTGCCATTGAGGGTGACAAGTGTCACCCATGAATTTGGTCACTCGTCAGCACTCTCTTAGTT
66 TTTTTGCCATTGAGGGTGACAAGTGTCACCCATGAATTTGGTCACTCGCCAACACTCTCTTAGTT
2880 AGGATTGCTATTATATAGTGGTATTGATTGATCACATATAACTTGCTCAAGGGAGGTCATGCATG
131 AGGATTGCTATTATATAGTGGTATTGATTGATCACATATAACTTGCTCAAGGGAGGTCATGCATG
2945 CGAAATAAATTTCAACCCATTTCCATTTCAGAAGTCAAATCCAACCATTTAGTCATTGGAACAAA
196 CGAAATAAATTTCAACCCATTTCCATTTCAGAAGTCAAATCCAACCATTTAGTCATTGGAACAAA
3010 AAAAAACCCTAAAATGCATTACAGAAAACCTCAAGTCCAAAATCCATTACAGAAAACCCTGAAGT
261 AAAAAACCCTAAAATGCATTACAGAAAACCTCAAGTCCAAAATCCATTACAGAAAACCCTGAAGT
3075 CCGAGTAAATGAAAACCAT
326 CCGAGTAAATGAAAACCAT
3094 AAATATCAAAGGGACACATGAGCATAAAATTGAAATGTTTGAAGACTATTTCATAAATAACCCCT
1 AAATATCAAAGGGACACATGAGCATAAAATTGAAATGTTTGAAGACTATTTCATAAATAACCCCT
3159 TTTTTGCCATTGAGGGTGACAAGTGTCACCCATGAATTTGGTCACTCGCCAACACTCTCTTAGTT
66 TTTTTGCCATTGAGGGTGACAAGTGTCACCCATGAATTTGGTCACTCGCCAACACTCTCTTAGTT
*
3224 AGGATTGCTATTATATAGTGGTATTGATTGATCTCATATAACTTGCTCAAGGGAGGTCATGCATG
131 AGGATTGCTATTATATAGTGGTATTGATTGATCACATATAACTTGCTCAAGGGAGGTCATGCATG
3289 CGAAATAAATTTCAACCCATTTCCATTTCAGAAGTCAAATCCAACCATTTAGTCATTGGAACAAA
196 CGAAATAAATTTCAACCCATTTCCATTTCAGAAGTCAAATCCAACCATTTAGTCATTGGAACAAA
3354 AAAAAACCCTAAAATGCATTACAGAAAACCTCAAGTCCAAAATCCATTACAGAAAACCCTGAAGT
261 AAAAAACCCTAAAATGCATTACAGAAAACCTCAAGTCCAAAATCCATTACAGAAAACCCTGAAGT
3419 CCGAGTAAATGAAAACCAT
326 CCGAGTAAATGAAAACCAT
3438 A
1 A
3439 GCCTAATCCG
Statistics
Matches: 342, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
344 342 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (344 bp):
AAATATCAAAGGGACACATGAGCATAAAATTGAAATGTTTGAAGACTATTTCATAAATAACCCCT
TTTTTGCCATTGAGGGTGACAAGTGTCACCCATGAATTTGGTCACTCGCCAACACTCTCTTAGTT
AGGATTGCTATTATATAGTGGTATTGATTGATCACATATAACTTGCTCAAGGGAGGTCATGCATG
CGAAATAAATTTCAACCCATTTCCATTTCAGAAGTCAAATCCAACCATTTAGTCATTGGAACAAA
AAAAAACCCTAAAATGCATTACAGAAAACCTCAAGTCCAAAATCCATTACAGAAAACCCTGAAGT
CCGAGTAAATGAAAACCAT
Found at i:3395 original size:28 final size:29
Alignment explanation
Indices: 3364--3420 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
3354 AAAAAACCCT
*
3364 AAAATGCATTACAGAAAA-CCTCAAGTCC
1 AAAATCCATTACAGAAAACCCTCAAGTCC
*
3392 AAAATCCATTACAGAAAACCCTGAAGTCC
1 AAAATCCATTACAGAAAACCCTCAAGTCC
3421 GAGTAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.18
Consensus pattern (29 bp):
AAAATCCATTACAGAAAACCCTCAAGTCC
Done.