Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018972.1 Corchorus olitorius cultivar O-4 contig19005, 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: 27506
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4598 original size:19 final size:18
Alignment explanation
Indices: 4565--4600 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4555 TCGAGATAAT
4565 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
4583 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
4601 TAAGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7726 original size:35 final size:36
Alignment explanation
Indices: 7682--7750 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 36
7672 TTATTAGTAT
7682 TTAATTTTTA-TTCAACCATTAATAA-A-TATATAGG
1 TTAATTTTTATTTCAA-CATTAATAATATTATATAGG
*
7716 TTAATATTTTATTTCAATATTAATAATATTATATA
1 TTAAT-TTTTATTTCAACATTAATAATATTATATA
7751 CACATACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 5 0.17
35 13 0.43
36 6 0.20
37 6 0.20
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (36 bp):
TTAATTTTTATTTCAACATTAATAATATTATATAGG
Found at i:7934 original size:21 final size:21
Alignment explanation
Indices: 7905--7945 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7895 TTATATTCTC
*
7905 ATCTATACAGTGTCTAATCTG
1 ATCTATACAATGTCTAATCTG
* *
7926 ATCTGTACAATGTTTAATCT
1 ATCTATACAATGTCTAATCT
7946 CACAGCTCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATCTATACAATGTCTAATCTG
Found at i:9112 original size:31 final size:31
Alignment explanation
Indices: 9074--9155 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
9064 ATTACAAAAA
*
9074 CAAGCAATTAAGGTTATAATGTTTTCAATTT
1 CAAGCAATTAAGGATATAATGTTTTCAATTT
* *
9105 CAAGCAATTAAGAATATAACGTTTTCAATTT
1 CAAGCAATTAAGGATATAATGTTTTCAATTT
9136 CAAGCAATTAAGGATATAAT
1 CAAGCAATTAAGGATATAAT
9156 CAGTTAGGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAATGTTTTCAATTT
Found at i:10170 original size:14 final size:14
Alignment explanation
Indices: 10151--10177 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10141 ATATTGTGGC
10151 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
10165 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
10178 AAAGACTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:11555 original size:16 final size:16
Alignment explanation
Indices: 11534--11606 Score: 94
Period size: 16 Copynumber: 4.6 Consensus size: 16
11524 GGGCGTCGGG
* *
11534 CGGGTTAGGGTTTTTT
1 CGGGTTCGGGTATTTT
11550 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
11566 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
11582 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
11598 CGGGTTCGG
1 CGGGTTCGG
11607 TCTCGAGTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.02
16 47 0.96
17 1 0.02
ACGTcount: A:0.05, C:0.14, G:0.41, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:11792 original size:13 final size:12
Alignment explanation
Indices: 11769--11815 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
11759 AAGTTTATTG
11769 ATAATATATAAT
1 ATAATATATAAT
11781 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
11794 ATAACAT-TATT
1 ATAATATATAAT
11805 ATCAATATATA
1 AT-AATATATA
11816 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:12448 original size:23 final size:23
Alignment explanation
Indices: 12400--12449 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12390 TATAATATTT
* *
12400 ATAAAAATATTGAATTTAATTAA
1 ATAAAAATATAGAATTTAAGTAA
*
12423 ATAAAAATATAG-ATTTCAGTAGA
1 ATAAAAATATAGAATTTAAGTA-A
12446 ATAA
1 ATAA
12450 TTATAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (23 bp):
ATAAAAATATAGAATTTAAGTAA
Found at i:12896 original size:2 final size:2
Alignment explanation
Indices: 12883--12915 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
12873 GTACTTTTTA
12883 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
12916 TTAAGAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23131 original size:51 final size:50
Alignment explanation
Indices: 23030--23132 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
23020 GTTCTTCATA
* *
23030 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
* * *
23080 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGT
23131 TT
1 TT
23133 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
Found at i:25645 original size:21 final size:21
Alignment explanation
Indices: 25619--25658 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25609 CAACAAAGAG
* *
25619 GGAGATGCTTCCTTCCTCCTA
1 GGAGATGCCTCCTACCTCCTA
25640 GGAGATGCCTCCTACCTCC
1 GGAGATGCCTCCTACCTCC
25659 CAAGAGGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.38, G:0.20, T:0.28
Consensus pattern (21 bp):
GGAGATGCCTCCTACCTCCTA
Found at i:25812 original size:28 final size:28
Alignment explanation
Indices: 25772--25981 Score: 246
Period size: 28 Copynumber: 7.5 Consensus size: 28
25762 CTTTGTTTCT
25772 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
25800 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * * *
25828 TATTTTGGTCATTCTACAAGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
25856 CATTTTGGTCATTCTTTCAGGTCCAGGGGG
1 CATTTTGGTCATT-TTTCATGTCCA-GGGG
* * *
25886 CGTTGTGGTCATTATTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* *
25914 TATTTTGGTCA-TTTGCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
* * *
25941 TATTTTGGTCA-TTTGCACGTCC-GGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
25967 ACATTTTAGTCATTT
1 -CATTTTGGTCATTT
25982 CATGCACATT
Statistics
Matches: 158, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.03
27 44 0.28
28 78 0.49
29 17 0.11
30 15 0.09
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Found at i:25915 original size:86 final size:83
Alignment explanation
Indices: 25772--25954 Score: 276
Period size: 86 Copynumber: 2.2 Consensus size: 83
25762 CTTTGTTTCT
* * *
25772 CATTTTGGTCATTTTTCATGTCCAGGGGCATTTTGGTCATTTTTCATGTCCAGGGGTATTTTGGT
1 CATTTTGGTCATTTTTCAGGTCCAGGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTGGT
25837 CATTCTACAAGTCCAGGGG
66 CATT-TACAAGTCCAGGGG
*
25856 CATTTTGGTCATTCTTTCAGGTCCAGGGGGCGTTGTGGTCATTATTCATGTCCAGGGGTATTTTG
1 CATTTTGGTCATT-TTTCAGGTCCA-GGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTG
* *
25921 GTCATTTGCATGTCCAGGGG
64 GTCATTTACAAGTCCAGGGG
*
25941 TATTTTGGTCATTT
1 CATTTTGGTCATTT
25955 GCACGTCCGG
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
84 14 0.16
85 34 0.38
86 42 0.47
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (83 bp):
CATTTTGGTCATTTTTCAGGTCCAGGGGCATTGTGGTCATTATTCATGTCCAGGGGTATTTTGGT
CATTTACAAGTCCAGGGG
Done.