Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001611.1 Corchorus capsularis cultivar CVL-1 contig01611, 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, 804
Length: 1340
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:199 original size:23 final size:23
Alignment explanation
Indices: 160--221 Score: 106
Period size: 23 Copynumber: 2.6 Consensus size: 23
150 GAGTGGCCTT
160 TTATTTATTTATTTATATTTATTGA
1 TTATTTA--TATTTATATTTATTGA
185 TTATTTATATTTATATTTATTGA
1 TTATTTATATTTATATTTATTGA
208 TTATTTATATTTAT
1 TTATTTATATTTAT
222 CGTATATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 30 0.81
25 7 0.19
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (23 bp):
TTATTTATATTTATATTTATTGA
Found at i:229 original size:17 final size:17
Alignment explanation
Indices: 190--231 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
180 ATTGATTATT
*
190 TATATTTATATTTATTG
1 TATATTTATATTTATCG
207 -ATTATTTATATTTATCG
1 TA-TATTTATATTTATCG
224 TATATTTA
1 TATATTTA
232 CTTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (17 bp):
TATATTTATATTTATCG
Found at i:1126 original size:24 final size:24
Alignment explanation
Indices: 1094--1176 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 24
1084 CATATAATAA
*
1094 TCAATAATGATGAAATTCTAAATT
1 TCAAAAATGATGAAATTCTAAATT
* *
1118 TC-AAAA--ATGAATTATCATATAATAA
1 TCAAAAATGATGAAAT-TC-TA-AAT-T
*
1143 TCAATAATGATGAAATTCTAAATT
1 TCAAAAATGATGAAATTCTAAATT
1167 TCAAAAATGA
1 TCAAAAATGA
1177 ATTATCATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
21 6 0.13
22 2 0.04
23 5 0.11
24 14 0.31
25 5 0.11
26 5 0.11
27 2 0.04
28 6 0.13
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (24 bp):
TCAAAAATGATGAAATTCTAAATT
Found at i:1140 original size:49 final size:49
Alignment explanation
Indices: 1068--1192 Score: 250
Period size: 49 Copynumber: 2.6 Consensus size: 49
1058 AAAATCATCA
1068 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
1117 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
1 TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
1166 TTCAAAAATGAATTATCATATAATAAT
1 TTCAAAAATGAATTATCATATAATAAT
1193 TAATTATCAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (49 bp):
TTCAAAAATGAATTATCATATAATAATCAATAATGATGAAATTCTAAAT
Found at i:1217 original size:21 final size:18
Alignment explanation
Indices: 1176--1210 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1166 TTCAAAAATG
1176 AATTATCATATAATAATT
1 AATTATCATATAATAATT
1194 AATTATCATATAATAAT
1 AATTATCATATAATAAT
1211 CAATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTATCATATAATAATT
Found at i:1306 original size:21 final size:21
Alignment explanation
Indices: 1282--1323 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1272 AGGATATAAT
1282 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
1303 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
1324 AGAGATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Done.