Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012100.1 Corchorus olitorius cultivar O-4 contig12133, 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: 35224
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Found at i:9993 original size:21 final size:21
Alignment explanation
Indices: 9967--10009 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9957 CCAATAAAAC
9967 CTATCCAGAGTGACCTTGGCT
1 CTATCCAGAGTGACCTTGGCT
9988 CTATCCAGAGTGACCTTGGCT
1 CTATCCAGAGTGACCTTGGCT
10009 C
1 C
10010 GAGTCAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (21 bp):
CTATCCAGAGTGACCTTGGCT
Found at i:12468 original size:2 final size:2
Alignment explanation
Indices: 12461--12491 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12451 TGGCTGGTTA
12461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12492 GTAAAAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17090 original size:30 final size:31
Alignment explanation
Indices: 17056--17122 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 31
17046 AGTAAGTTTA
*
17056 CCTTT-AAATGCCATCTCTGAAGGTTTTTTC
1 CCTTTAAAACGCCATCTCTGAAGGTTTTTTC
17086 CCTTTCAAAACGCCATCTCTGAAGGTTTTTTC
1 CCTTT-AAAACGCCATCTCTGAAGGTTTTTTC
17118 CCTTT
1 CCTTT
17123 TAATTCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 5 0.15
32 29 0.85
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (31 bp):
CCTTTAAAACGCCATCTCTGAAGGTTTTTTC
Found at i:17350 original size:18 final size:18
Alignment explanation
Indices: 17324--17360 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17314 TCTTTAAAAG
*
17324 TTTATAGCCATATTTTTC
1 TTTAGAGCCATATTTTTC
17342 TTTAGAGCCATATTTTTC
1 TTTAGAGCCATATTTTTC
17360 T
1 T
17361 GTTCAAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTAGAGCCATATTTTTC
Found at i:21643 original size:2 final size:2
Alignment explanation
Indices: 21636--21664 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21626 TATGATATGT
21636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21665 GAATCTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21777 original size:14 final size:15
Alignment explanation
Indices: 21752--21785 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21742 GGAAGAAAAT
21752 TGTTGCTTTAATCTG
1 TGTTGCTTTAATCTG
*
21767 TGTTG-TTTAATTTG
1 TGTTGCTTTAATCTG
21781 TGTTG
1 TGTTG
21786 ATTGAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.59
Consensus pattern (15 bp):
TGTTGCTTTAATCTG
Found at i:23132 original size:43 final size:44
Alignment explanation
Indices: 23065--23165 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 44
23055 TAGTTAGGTT
* * * * * *
23065 ATCAAAGTTTCTTATGGAGTTTATCACAATTTTATA-GTTACTA
1 ATCAAAATTTCATATGGAGATTATCAAAATTTAATAGGGTACTA
* * *
23108 ATCAAAATTTCATATGGTGATTATCAAAATTTAATAGGGTAGTT
1 ATCAAAATTTCATATGGAGATTATCAAAATTTAATAGGGTACTA
23152 ATCAAAATTTCATA
1 ATCAAAATTTCATA
23166 AAAATATTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 30 0.62
44 18 0.38
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.41
Consensus pattern (44 bp):
ATCAAAATTTCATATGGAGATTATCAAAATTTAATAGGGTACTA
Found at i:23134 original size:22 final size:22
Alignment explanation
Indices: 23108--23165 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
23098 ATAGTTACTA
*
23108 ATCAAAATTTCATATGGT-GATT
1 ATCAAAATTTCATAGGGTAG-TT
*
23130 ATCAAAATTTAATAGGGTAGTT
1 ATCAAAATTTCATAGGGTAGTT
23152 ATCAAAATTTCATA
1 ATCAAAATTTCATA
23166 AAAATATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGTAGTT
Found at i:27003 original size:1 final size:1
Alignment explanation
Indices: 26997--27021 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
26987 AAGTACATAA
26997 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
27022 CAGAATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29526 original size:13 final size:13
Alignment explanation
Indices: 29508--29533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29498 AAGGTAACAA
29508 CAAAAATCATCAC
1 CAAAAATCATCAC
29521 CAAAAATCATCAC
1 CAAAAATCATCAC
29534 TCAAGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.