Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014693.1 Corchorus olitorius cultivar O-4 contig14726, 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: 57417
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1410 original size:29 final size:29
Alignment explanation
Indices: 1335--1412 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 29
1325 ACTTGTAGCG
**
1335 TTTGGACATTTTGTCCCCCCGAACTTCAAT
1 TTTGGACATTTTG-CCCCCTAAACTTCAAT
1365 TTTGGACATTTTGCCCCCTAAACTCTCAAT
1 TTTGGACATTTTGCCCCCTAAACT-TCAAT
*
1395 TTTGGACCTTTT-CCCCCT
1 TTTGGACATTTTGCCCCCT
1413 CTCAAATGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.34
30 29 0.66
ACGTcount: A:0.18, C:0.32, G:0.12, T:0.38
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCCTAAACTTCAAT
Found at i:1588 original size:29 final size:29
Alignment explanation
Indices: 1538--1599 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
1528 GGGCATAACA
*
1538 TCCAAAATTGAGAGTTCAGGGACAAAATG
1 TCCAAAATTGAGAGTTCAGGGACAAAACG
1567 TCCAAAATTGA-AGTTCAGGGGACAAAACG
1 TCCAAAATTGAGAGTTCA-GGGACAAAACG
1596 TCCA
1 TCCA
1600 GATGCTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (29 bp):
TCCAAAATTGAGAGTTCAGGGACAAAACG
Found at i:4765 original size:25 final size:25
Alignment explanation
Indices: 4717--4767 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
4707 TTGATGATAT
**
4717 AACTTGTTTGAATTTTCCTAAAAAA
1 AACTTGTTTGAATTTTAATAAAAAA
4742 AACTTGTTTGAATTCTTAATAAAAAA
1 AACTTGTTTGAATT-TTAATAAAAAA
4768 TTTGCTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (25 bp):
AACTTGTTTGAATTTTAATAAAAAA
Found at i:7219 original size:36 final size:36
Alignment explanation
Indices: 7178--7251 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
7168 GTGTTGCCAG
*
7178 CATGGTGAATTTTCACATCAACGCCTTCATGACAGC
1 CATGGTGAACTTTCACATCAACGCCTTCATGACAGC
* *
7214 CATGGTGAACTTTCACATCAATGCCTTCATGGCAGC
1 CATGGTGAACTTTCACATCAACGCCTTCATGACAGC
7250 CA
1 CA
7252 AAATTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (36 bp):
CATGGTGAACTTTCACATCAACGCCTTCATGACAGC
Found at i:8132 original size:30 final size:30
Alignment explanation
Indices: 8098--8159 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
8088 GTTAATAAGC
8098 CATTAAAATTTAAGGGTATAAGAGAAAAGT
1 CATTAAAATTTAAGGGTATAAGAGAAAAGT
* *
8128 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTAAGGGTATAAGAGAAAAGT
8158 CA
1 CA
8160 AGATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTAAGGGTATAAGAGAAAAGT
Found at i:11536 original size:40 final size:38
Alignment explanation
Indices: 11481--11560 Score: 133
Period size: 40 Copynumber: 2.1 Consensus size: 38
11471 TTATTTTAAG
*
11481 AAACAAGATCAAATATCTTTTCATAAAATCCTCTATATAT
1 AAACAAGATCAAATATC-TTTCAT-AAATCCTCTATAAAT
11521 AAACAAGATCAAATATCTTTCATAAATCCTCTATAAAT
1 AAACAAGATCAAATATCTTTCATAAATCCTCTATAAAT
11559 AA
1 AA
11561 GTAGTTACTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 16 0.41
39 6 0.15
40 17 0.44
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (38 bp):
AAACAAGATCAAATATCTTTCATAAATCCTCTATAAAT
Found at i:13269 original size:30 final size:30
Alignment explanation
Indices: 13233--13293 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
13223 TGATTAGTGG
13233 AAGTCTAATTGAAATACAAGCCTTCACCCA
1 AAGTCTAATTGAAATACAAGCCTTCACCCA
13263 AAGTCTAATTGAAATACAAGCCTTCACCCA
1 AAGTCTAATTGAAATACAAGCCTTCACCCA
13293 A
1 A
13294 TTTCTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (30 bp):
AAGTCTAATTGAAATACAAGCCTTCACCCA
Found at i:15127 original size:13 final size:13
Alignment explanation
Indices: 15095--15127 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15085 AAAAAACATG
15095 ATTAAGGAGATTA
1 ATTAAGGAGATTA
*
15108 ATT-AGGAGTTTA
1 ATTAAGGAGATTA
15120 ATTAAGGA
1 ATTAAGGA
15128 TCAATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (13 bp):
ATTAAGGAGATTA
Found at i:38138 original size:10 final size:9
Alignment explanation
Indices: 38111--38140 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
38101 ATAGAAGAAA
*
38111 TTATTTGTT
1 TTATTTTTT
38120 TTATTTTTT
1 TTATTTTTT
38129 TTATTTTTT
1 TTATTTTTT
38138 TTA
1 TTA
38141 AAGAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (9 bp):
TTATTTTTT
Found at i:38359 original size:15 final size:15
Alignment explanation
Indices: 38341--38374 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38331 TTTGGGGTTG
38341 GATTTTATTTGATTT
1 GATTTTATTTGATTT
*
38356 GATTTTATTTTATTT
1 GATTTTATTTGATTT
38371 -ATTT
1 GATTT
38375 ATAGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (15 bp):
GATTTTATTTGATTT
Done.