Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009720.1 Corchorus olitorius cultivar O-4 contig09752, 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:0.35, C:0.14, G:0.14, T:0.36
Found at i:258 original size:31 final size:31
Alignment explanation
Indices: 223--291 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
213 AATTTGATTA
223 CAGGGACTTAATTGCACAATTAATTAATATT
1 CAGGGACTTAATTGCACAATTAATTAATATT
* *
254 CAGGGACTTATTTGTACAATTAATTAATATT
1 CAGGGACTTAATTGCACAATTAATTAATATT
285 CAGGGAC
1 CAGGGAC
292 CTAAGATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (31 bp):
CAGGGACTTAATTGCACAATTAATTAATATT
Found at i:1348 original size:22 final size:21
Alignment explanation
Indices: 1315--1372 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
1305 ATTATTAATT
1315 ATAATTAATAATAACAATTTAA
1 ATAATTAATAATAACAA-TTAA
*
1337 ATTAA-TAATAATTAATAATTAA
1 A-TAATTAATAA-TAACAATTAA
1359 ATAATTAATAATAA
1 ATAATTAATAATAA
1373 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAATAATAACAATTAA
Found at i:1354 original size:7 final size:7
Alignment explanation
Indices: 1296--1370 Score: 66
Period size: 7 Copynumber: 10.6 Consensus size: 7
1286 TTTTGTTTTT
*
1296 TAATTAT
1 TAATTAA
*
1303 TAATTAT
1 TAATTAA
1310 TAATT-A
1 TAATTAA
1316 TAATTAA
1 TAATTAA
1323 TAA-TAA
1 TAATTAA
*
1329 CAATTTAAA
1 TAA-TT-AA
1338 TTAA-TAA
1 -TAATTAA
1345 TAATTAA
1 TAATTAA
1352 TAATTAAA
1 TAATT-AA
1360 TAATTAA
1 TAATTAA
1367 TAAT
1 TAAT
1371 AATTAAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
6 13 0.22
7 32 0.55
8 9 0.16
9 2 0.03
10 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:1384 original size:25 final size:25
Alignment explanation
Indices: 1336--1384 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1326 TAACAATTTA
* *
1336 AATTAATAATAATTAATAATTAAAT
1 AATTAATAATAATTAAAAAATAAAT
1361 AATTAATAATAATTAAAAAATAAA
1 AATTAATAATAATTAAAAAATAAA
1385 AAAAATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAATAATAATTAAAAAATAAAT
Found at i:1970 original size:174 final size:174
Alignment explanation
Indices: 1651--2069 Score: 675
Period size: 174 Copynumber: 2.4 Consensus size: 174
1641 AGCAATTCAG
1651 TTTT-TTTATTGCAATAAATATTGATGGACCATTTACAGATGACAATAGAAGACATCCTACTTTT
1 TTTTGTTT-TTGCAATAAATATTGATGGACCATTTACAGATGACAATAGAAGACATCCTACTTTT
*
1715 TCTAAGT-AAGAAAAAATATTAAAATATGGAATTATTATCTAAAGTAAAATCACATTTATTTGAG
65 TCTAAGTAAAAAAAAAATATTAAAATATGGAATTATTATCTAAAGTAAAATCACATTTATTTGAG
*
1779 GACCTATTATCCAATTAATAATCATTAGTCGATATTAATGGA-CA
130 GACCTAATATCCAATTAATAATCATTAGTCGATATTAATGGACCA
* * *
1823 -TTTGTTTTTGCAATAAATATTGATGGACTATTTACATATGACAATAGAAGACATCCTACTTTCT
1 TTTTGTTTTTGCAATAAATATTGATGGACCATTTACAGATGACAATAGAAGACATCCTACTTTTT
1887 CTAAGTAACAAAAAAAATTATTAAAATATGGAATTATTATCTAAAGTAAAATCACATTTATTTGA
66 CTAAGTAA-AAAAAAAA-TATTAAAATATGGAATTATTATCTAAAGTAAAATCACATTTATTTGA
*
1952 GGACTTAATATCCAATTAATAATCATTAGTCGATATTAATGGACCA
129 GGACCTAATATCCAATTAATAATCATTAGTCGATATTAATGGACCA
* * * * * *
1998 TTTTTTTTTTGCAATGAATATTAATGGACCATTTACGGATGACAATAGAAAACATCCTGCTTTTT
1 TTTTGTTTTTGCAATAAATATTGATGGACCATTTACAGATGACAATAGAAGACATCCTACTTTTT
2063 CTAAGTA
66 CTAAGTA
2070 TAAATTAAAA
Statistics
Matches: 226, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
171 63 0.28
172 4 0.02
173 7 0.03
174 88 0.39
175 2 0.01
176 62 0.27
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (174 bp):
TTTTGTTTTTGCAATAAATATTGATGGACCATTTACAGATGACAATAGAAGACATCCTACTTTTT
CTAAGTAAAAAAAAAATATTAAAATATGGAATTATTATCTAAAGTAAAATCACATTTATTTGAGG
ACCTAATATCCAATTAATAATCATTAGTCGATATTAATGGACCA
Found at i:2903 original size:7 final size:6
Alignment explanation
Indices: 2877--2918 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
2867 CTTGTCATCT
*
2877 TTTTC- TTTTC- TTTTCTT TTTTCA TTTTCA TTTTCA TTTTCA T
1 TTTTCA TTTTCA TTTTC-A TTTTCA TTTTCA TTTTCA TTTTCA T
2919 ATCTCTCTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 10 0.29
6 19 0.56
7 5 0.15
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCA
Found at i:3258 original size:107 final size:107
Alignment explanation
Indices: 3147--3339 Score: 307
Period size: 107 Copynumber: 1.8 Consensus size: 107
3137 TTTTTATTAC
* * *
3147 AGGGTTTTAGAAATAAAATATAAAACTAATTTTACTAGGTTTAGCCCCAAATTAACATTTTAATT
1 AGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT-ATT
3212 -TTATTTTAAGGGTAAATTCCAAAATTAATAACTTATTGTTAT
65 GTTATTTTAAGGGTAAATTCCAAAATTAATAACTTATTGTTAT
* **
3254 AGGGTTTTATAAATAAAATATAAAACTAATTTCACTAAGTTTAGGTCCAAATTAAAATTTTATTG
1 AGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTG
*
3319 TTATTTTATGGGTAAATTCCA
66 TTATTTTAAGGGTAAATTCCA
3340 TAATATTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 3 0.04
107 75 0.96
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (107 bp):
AGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTG
TTATTTTAAGGGTAAATTCCAAAATTAATAACTTATTGTTAT
Done.