Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020336.1 Corchorus olitorius cultivar O-4 contig20369, 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: 23529
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7144 original size:36 final size:36
Alignment explanation
Indices: 7097--7186 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
7087 TATGCATTTT
7097 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
1 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
* *
7133 TTATTAGTAATTAGGCATCATCGTTCACGTTAGTAA
1 TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
7169 TTATTAGTAATTAGGCAT
1 TTATTAGTAATTAGGCAT
7187 TGCATTCACA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (36 bp):
TTATTAGTAATTAGGCATCATCATTCACATTAGTAA
Found at i:10593 original size:30 final size:33
Alignment explanation
Indices: 10521--10607 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 33
10511 AAGTAAAATC
*
10521 CCAAAAGAAGATTTTGGAAAATAAAGTTTGGATAATT
1 CCAAAAGGAGATTTTGGAAAATAAA---T-GATAATT
10558 CCAAAAGGAGATTTTGGAAAATAAA-GA-AATT
1 CCAAAAGGAGATTTTGGAAAATAAATGATAATT
10589 -CAAAAGGAGATTTTGGAAA
1 CCAAAAGGAGATTTTGGAAA
10608 TTAATAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 19 0.39
31 4 0.08
32 2 0.04
37 24 0.49
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (33 bp):
CCAAAAGGAGATTTTGGAAAATAAATGATAATT
Found at i:12814 original size:66 final size:66
Alignment explanation
Indices: 12727--12858 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
12717 ATAGTTGTAA
*
12727 ATGAGCAGGCTTCTCTGCCTCAGCCTTACTCTTGCAAGCTCAAGAATGATGTTATTGTTAGGAGC
1 ATGAACAGGCTTCTCTGCCTCAGCCTTACTCTTGCAAGCTCAAGAATGATGTTATTGTTAGGAGC
12792 T
66 T
12793 ATGAACAGGCTTCTCTGCCTCAGCCTTACTCTTGCAAGCTCAAGAATGATGTTATTGTTAGGAGC
1 ATGAACAGGCTTCTCTGCCTCAGCCTTACTCTTGCAAGCTCAAGAATGATGTTATTGTTAGGAGC
12858 T
66 T
12859 TTGCAGACTG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (66 bp):
ATGAACAGGCTTCTCTGCCTCAGCCTTACTCTTGCAAGCTCAAGAATGATGTTATTGTTAGGAGC
T
Found at i:13425 original size:13 final size:13
Alignment explanation
Indices: 13407--13433 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13397 TAGCTTGATC
13407 TCGATGCAATGGA
1 TCGATGCAATGGA
13420 TCGATGCAATGGA
1 TCGATGCAATGGA
13433 T
1 T
13434 TTGAGAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (13 bp):
TCGATGCAATGGA
Found at i:13494 original size:42 final size:42
Alignment explanation
Indices: 13433--13513 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
13423 ATGCAATGGA
* *
13433 TTTGAGAGGAATGGTCGAAGGCTTGTTATTCCTCGTTGTGGC
1 TTTGAGAGAAATGGCCGAAGGCTTGTTATTCCTCGTTGTGGC
13475 TTTGAGAGAAATGGCCGAAGGCTTGTTATTCCTCGTTGT
1 TTTGAGAGAAATGGCCGAAGGCTTGTTATTCCTCGTTGT
13514 CGGATTTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.19, C:0.15, G:0.31, T:0.36
Consensus pattern (42 bp):
TTTGAGAGAAATGGCCGAAGGCTTGTTATTCCTCGTTGTGGC
Found at i:13638 original size:28 final size:28
Alignment explanation
Indices: 13606--13662 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
13596 ATTTTTAGAG
*
13606 AAAGAATCAAAGACTTGTTGTTTTCTGT
1 AAAGAATCAAAGACTTGTTATTTTCTGT
13634 AAAGAATCAAAGACTTGTTATTTTCTGT
1 AAAGAATCAAAGACTTGTTATTTTCTGT
13662 A
1 A
13663 GATCGGCTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (28 bp):
AAAGAATCAAAGACTTGTTATTTTCTGT
Found at i:13789 original size:26 final size:26
Alignment explanation
Indices: 13760--13842 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
13750 TTGCTGGTGG
13760 CTTGATGGAGAAGAACTTTGCCTTCC
1 CTTGATGGAGAAGAACTTTGCCTTCC
* * **
13786 CTTGAATTTGGAG-AG-ATTGTTG--GTGG
1 CTTG-A--TGGAGAAGAACT-TTGCCTTCC
13812 CTTGATGGAGAAGAACTTTGCCTTCC
1 CTTGATGGAGAAGAACTTTGCCTTCC
13838 CTTGA
1 CTTGA
13843 ATTTGGAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
23 5 0.12
24 5 0.12
25 3 0.07
26 15 0.37
27 3 0.07
28 5 0.12
29 5 0.12
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.34
Consensus pattern (26 bp):
CTTGATGGAGAAGAACTTTGCCTTCC
Found at i:13798 original size:29 final size:29
Alignment explanation
Indices: 13765--13851 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
13755 GGTGGCTTGA
13765 TGGAGAAGAACTTTGCCTTCCCTTGAATT
1 TGGAGAAGAACTTTGCCTTCCCTTGAATT
* * **
13794 TGGAG-AG-ATTGTTG--GTGGCTTG-A--
1 TGGAGAAGAACT-TTGCCTTCCCTTGAATT
13817 TGGAGAAGAACTTTGCCTTCCCTTGAATT
1 TGGAGAAGAACTTTGCCTTCCCTTGAATT
13846 TGGAGA
1 TGGAGA
13852 GATGAGATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
23 5 0.12
24 5 0.12
25 3 0.07
26 10 0.24
27 3 0.07
28 5 0.12
29 11 0.26
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (29 bp):
TGGAGAAGAACTTTGCCTTCCCTTGAATT
Found at i:13826 original size:52 final size:52
Alignment explanation
Indices: 13712--13854 Score: 242
Period size: 52 Copynumber: 2.8 Consensus size: 52
13702 GATTTGCTTT
13712 GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTT-----GATTGCTGGTG
1 GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTTGGAGAGATTGCTGGTG
*
13759 GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTTGGAGAGATTGTTGGTG
1 GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTTGGAGAGATTGCTGGTG
13811 GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTTGGAGAGAT
1 GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTTGGAGAGAT
13855 GAGATTGCTG
Statistics
Matches: 90, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
47 36 0.40
52 54 0.60
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (52 bp):
GCTTGATGGAGAAGAACTTTGCCTTCCCTTGAATTTGGAGAGATTGCTGGTG
Found at i:15463 original size:1 final size:1
Alignment explanation
Indices: 15457--15506 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
15447 GATATCAAAG
* * * * *
15457 AAAAAAACAAAAAAAAACAAAAAAAAACAAAAGAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15507 CATCTTTCAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:15470 original size:10 final size:10
Alignment explanation
Indices: 15457--15503 Score: 85
Period size: 10 Copynumber: 4.7 Consensus size: 10
15447 GATATCAAAG
15457 AAAAAAACAA
1 AAAAAAACAA
15467 AAAAAAACAA
1 AAAAAAACAA
15477 AAAAAAACAA
1 AAAAAAACAA
*
15487 AAGAAAACAA
1 AAAAAAACAA
15497 AAAAAAA
1 AAAAAAA
15504 AAACATCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:16191 original size:19 final size:20
Alignment explanation
Indices: 16164--16201 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16154 TTTATCCTCT
16164 AATGAGTAG-TTTTATTTTA
1 AATGAGTAGTTTTTATTTTA
*
16183 AATGGGTAGTTTTTATTTT
1 AATGAGTAGTTTTTATTTT
16202 GTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (20 bp):
AATGAGTAGTTTTTATTTTA
Found at i:20863 original size:405 final size:390
Alignment explanation
Indices: 20161--20941 Score: 1337
Period size: 390 Copynumber: 2.0 Consensus size: 390
20151 TGGGTTTTCT
20161 GGGTTTTGACTAGTTTTTGACAGGGTGGTTTGCTTAACGGGTTAGGGTCTTCTCCGAACAGCCAT
1 GGGTTTTGACTAGTTTTTGACAGGGTGGTTTGCTTAACGGGTTAGGGTCTTCTCCGAACAGCCAT
*
20226 GGCCTCCGGGCTCCGGACTAACAAGGTGGACCGACCGGTCTGGGCCAGGTACTCTAACACGGCCA
66 GGCCTCCGGGCTCCGGACTAACAAGGTGGAACGACCGGTCTGGGCCAGGTACTCTAACACGGCCA
20291 AAATCTAGTTCGCCTCATCTCGACACTACAATCCAATTCGTCAGTGACCATAACTGAGTCTTCGT
131 AAATCTAGTTCGCCTCATCTCGACACTACAATCCAATTCGTCAGTGACCATAACTGAGTCTTCGT
*
20356 GAGACCCCACCGCATCTTCACTCTTGCCTTTCAACAGTAAGCTCTCTCTCTCTCTTTTTGTATTC
196 GAGACCCCACCACATCTTCACTCTTGCCTTTCAACAGTAAGCTCTCTCTCTCTCTTTTTGTATTC
*
20421 TTTACTCTTCATAGCTTAAAAGTTTCCCTTTTAAAAAATATGATCTAACGAGATTCAAAATAATG
261 TTTACTCTTCATAGCTTAAAAGTTTCCCTTTTAAAAAATATGATCTAACGAGATTCAAAATAATA
*
20486 TCTCTGCTTTTTCAACAAACCAACCACACATTTCGTAAGGTAACATAAAATCTAGTTCGCCTAAC
326 TATCTGCTTTTTCAACAAACCAACCACACATTTCGTAAGGTAACATAAAATCTAGTTCGCCTAAC
* *
20551 GGGTTTTGACTAGTTTTTGACCGGGTGGTTTGCTTAACGGGTTAGGGTCTTCTCCGAACAGTCAT
1 GGGTTTTGACTAGTTTTTGACAGGGTGGTTTGCTTAACGGGTTAGGGTCTTCTCCGAACAGCCAT
* **
20616 GGCCTCCGGGCTTCGGACTAACAAGGTGGAACGACCGGTCTGGGCCAGGTACTCTAACACGGCTG
66 GGCCTCCGGGCTCCGGACTAACAAGGTGGAACGACCGGTCTGGGCCAGGTACTCTAACACGGCCA
20681 AAATCTAGTTCGCCTCATCTCGACACTACAATCCAATTCGTCAGTGACCATAACTGAGTCTTCGT
131 AAATCTAGTTCGCCTCATCTCGACACTACAATCCAATTCGTCAGTGACCATAACTGAGTCTTCGT
20746 GAGACCCCACCACATCTTCACTCTTGCCTTTCAACAGTAAGCTCTCTCTCTCTCTCTCTCGTTTT
196 GAGACCCCACCACATCTTCACTCTTGCCTTTCAACAGTAAG------CTCTCTCTCTCTC-----
20811 TTTTTTTTTGTATTCTTTACTCTTCATAGCTTAAAAGTTTCCCTTTTAAAAAATATGATCTAACG
250 ----TTTTTGTATTCTTTACTCTTCATAGCTTAAAAGTTTCCCTTTTAAAAAATATGATCTAACG
*
20876 AGATTCAAAATAATATATCTGCTTTTTTAACAAACCAACCACACATTTCGTAAGGTAACATAAAA
311 AGATTCAAAATAATATATCTGCTTTTTCAACAAACCAACCACACATTTCGTAAGGTAACATAAAA
20941 T
376 T
20942 ACGTACCTTT
Statistics
Matches: 366, Mismatches: 10, Indels: 15
0.94 0.03 0.04
Matches are distributed among these distances:
390 229 0.63
396 13 0.04
405 124 0.34
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (390 bp):
GGGTTTTGACTAGTTTTTGACAGGGTGGTTTGCTTAACGGGTTAGGGTCTTCTCCGAACAGCCAT
GGCCTCCGGGCTCCGGACTAACAAGGTGGAACGACCGGTCTGGGCCAGGTACTCTAACACGGCCA
AAATCTAGTTCGCCTCATCTCGACACTACAATCCAATTCGTCAGTGACCATAACTGAGTCTTCGT
GAGACCCCACCACATCTTCACTCTTGCCTTTCAACAGTAAGCTCTCTCTCTCTCTTTTTGTATTC
TTTACTCTTCATAGCTTAAAAGTTTCCCTTTTAAAAAATATGATCTAACGAGATTCAAAATAATA
TATCTGCTTTTTCAACAAACCAACCACACATTTCGTAAGGTAACATAAAATCTAGTTCGCCTAAC
Done.