Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016055.1 Corchorus olitorius cultivar O-4 contig16088, 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: 28880
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:3434 original size:25 final size:24
Alignment explanation
Indices: 3397--3443 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
3387 CTAGAAAATT
3397 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
3423 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
3444 AATAGAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:4406 original size:42 final size:42
Alignment explanation
Indices: 4347--4430 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
4337 CTCCAATGAT
4347 CTCCTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
1 CTCCTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
4389 CTCCTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
1 CTCCTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
4431 ATTTAGCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (42 bp):
CTCCTAGCATCTTCAAGACCATGATGAGTCCTTGGCGCATCA
Found at i:7176 original size:45 final size:45
Alignment explanation
Indices: 7126--7211 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
7116 TGACTATCGT
*
7126 AATAAAAGATGAAAAAAGTAAGAAGAGAAGAAGAGAAGATTGGAG
1 AATAAAAGATGAAAAAAGTAAGAAAAGAAGAAGAGAAGATTGGAG
7171 AATAAAAGATGAAAAAAGTAAGAAAAGAAGAAGAGAAGATT
1 AATAAAAGATGAAAAAAGTAAGAAAAGAAGAAGAGAAGATT
7212 TAGATGATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.12
Consensus pattern (45 bp):
AATAAAAGATGAAAAAAGTAAGAAAAGAAGAAGAGAAGATTGGAG
Found at i:11725 original size:21 final size:22
Alignment explanation
Indices: 11680--11728 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
11670 TCTTCAAATT
11680 TTAATAAAATCATAATTAATAA
1 TTAATAAAATCATAATTAATAA
11702 TTAATAAAA-CAT-ATTAATATA
1 TTAATAAAATCATAATTAATA-A
11723 TTAATA
1 TTAATA
11729 CATAATAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.27
21 10 0.38
22 9 0.35
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATAAAATCATAATTAATAA
Found at i:11800 original size:3 final size:3
Alignment explanation
Indices: 11794--11862 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
11784 ATAATTCAAT
* * * * *
11794 TAA TAA TAA TAA TAA TAA CAT TAA TAA TAA TAA TAA CAT TAC TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
11840 TAA TTA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
11863 AACCTAATTA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.94
4 2 0.04
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11828 original size:18 final size:18
Alignment explanation
Indices: 11797--11862 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
11787 ATTCAATTAA
11797 TAATAATAATAATAACAT
1 TAATAATAATAATAACAT
11815 TAATAATAATAATAACAT
1 TAATAATAATAATAACAT
*
11833 TACTACATAAT--TAA-A-
1 TAATA-ATAATAATAACAT
11848 TAATAATAATAATAA
1 TAATAATAATAATAA
11863 AACCTAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.12
15 4 0.09
16 4 0.09
17 3 0.07
18 22 0.51
19 5 0.12
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAATAATAATAACAT
Found at i:11870 original size:27 final size:26
Alignment explanation
Indices: 11784--11874 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 26
11774 CTATTTCATA
11784 ATAATTCAATTAATAATAATAATAATAAC
1 ATAATT-AA-TAATAATAATAATAA-AAC
* * **
11813 ATTAA-TAATAATAATAACATTACTAC
1 A-TAATTAATAATAATAATAATAAAAC
11839 ATAATTAAATAATAATAATAATAAAAC
1 ATAATT-AATAATAATAATAATAAAAC
*
11866 CTAATTAAT
1 ATAATTAAT
11875 CATTAAATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
25 3 0.06
26 7 0.14
27 33 0.66
28 2 0.04
29 2 0.04
30 3 0.06
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAATTAATAATAATAATAATAAAAC
Found at i:12013 original size:27 final size:27
Alignment explanation
Indices: 11975--12040 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
11965 AAAAAGGGCG
*
11975 GGTCGCGACCCACCGTCGGCCCTGGTC
1 GGTCGCGACCCACAGTCGGCCCTGGTC
* *
12002 GGTCACGACCCACAGTCGGCTCTGGTC
1 GGTCGCGACCCACAGTCGGCCCTGGTC
12029 GGTCGCGACCCA
1 GGTCGCGACCCA
12041 AGCTGATGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.12, C:0.41, G:0.32, T:0.15
Consensus pattern (27 bp):
GGTCGCGACCCACAGTCGGCCCTGGTC
Found at i:12607 original size:11 final size:11
Alignment explanation
Indices: 12591--12615 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12581 GTACATATGA
12591 AATCTCATTAC
1 AATCTCATTAC
12602 AATCTCATTAC
1 AATCTCATTAC
12613 AAT
1 AAT
12616 TAGATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (11 bp):
AATCTCATTAC
Found at i:14049 original size:2 final size:2
Alignment explanation
Indices: 14042--14071 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14032 TCATCATAAC
14042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14072 ATAACTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14156 original size:13 final size:13
Alignment explanation
Indices: 14138--14178 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
14128 ACCTTATTGA
14138 TCATCCGAAAGTT
1 TCATCCGAAAGTT
*
14151 TCATCC-AAA--A
1 TCATCCGAAAGTT
14161 TCATCCGAAAGTT
1 TCATCCGAAAGTT
14174 TCATC
1 TCATC
14179 AAAAAGCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 6 0.26
11 3 0.13
12 3 0.13
13 11 0.48
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (13 bp):
TCATCCGAAAGTT
Found at i:14167 original size:23 final size:23
Alignment explanation
Indices: 14137--14183 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
14127 AACCTTATTG
*
14137 ATCATCCGAAAGTTTCATCCAAA
1 ATCATCCGAAAGTTTCATCAAAA
14160 ATCATCCGAAAGTTTCATCAAAA
1 ATCATCCGAAAGTTTCATCAAAA
14183 A
1 A
14184 GCTTCGTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (23 bp):
ATCATCCGAAAGTTTCATCAAAA
Found at i:16869 original size:2 final size:2
Alignment explanation
Indices: 16862--16888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16852 ACAAAACCAC
16862 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 T
16889 TTGATGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18791 original size:100 final size:100
Alignment explanation
Indices: 18618--18813 Score: 365
Period size: 100 Copynumber: 2.0 Consensus size: 100
18608 TAAATTAGAT
*
18618 ATTAAGCCTAAAAAAGCACGCGTTCTTAGCTAAATGCTCAATTGAGGGCTCAACATTAGTGTGTT
1 ATTAAGCCTAAAAAAGCACACGTTCTTAGCTAAATGCTCAATTGAGGGCTCAACATTAGTGTGTT
18683 TGCTTAATTTTAACTCTAACCTTTTAATTTGAAAC
66 TGCTTAATTTTAACTCTAACCTTTTAATTTGAAAC
* *
18718 ATTAAGCCTACAAAAGTACACGTTCTTAGCTAAATGCTCAATTGAGGGCTCAACATTAGTGTGTT
1 ATTAAGCCTAAAAAAGCACACGTTCTTAGCTAAATGCTCAATTGAGGGCTCAACATTAGTGTGTT
18783 TGCTTAATTTTAACTCTAACCTTTTAATTTG
66 TGCTTAATTTTAACTCTAACCTTTTAATTTG
18814 TTCGATTGAG
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (100 bp):
ATTAAGCCTAAAAAAGCACACGTTCTTAGCTAAATGCTCAATTGAGGGCTCAACATTAGTGTGTT
TGCTTAATTTTAACTCTAACCTTTTAATTTGAAAC
Found at i:20436 original size:2 final size:2
Alignment explanation
Indices: 20429--20454 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20419 ACTATTAGAT
20429 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
20455 TGTATGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20949 original size:6 final size:6
Alignment explanation
Indices: 20938--20981 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
20928 AAGGCTGTAC
20938 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CACAAT CA
20982 TCCGTTAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Done.