Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014851.1 Corchorus olitorius cultivar O-4 contig14884, 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: 54228
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3176 original size:28 final size:28
Alignment explanation
Indices: 3136--3192 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3126 TGGTTTGATT
3136 ACAGTATTCTATTTCTTTCCAGTGAGTG
1 ACAGTATTCTATTTCTTTCCAGTGAGTG
3164 ACAGTATTCTATTTCTTTCCAGTGAGTG
1 ACAGTATTCTATTTCTTTCCAGTGAGTG
3192 A
1 A
3193 TTTTCTATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (28 bp):
ACAGTATTCTATTTCTTTCCAGTGAGTG
Found at i:3394 original size:14 final size:14
Alignment explanation
Indices: 3373--3407 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3363 CATCTTATGT
3373 TAAAATAATCCAAA
1 TAAAATAATCCAAA
*
3387 TGAAATAATCCAAA
1 TAAAATAATCCAAA
3401 TAAAATA
1 TAAAATA
3408 GTCTAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAATAATCCAAA
Found at i:10742 original size:16 final size:16
Alignment explanation
Indices: 10721--10753 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10711 CTTGAGTTCG
10721 AGTTCAATGAGTATGT
1 AGTTCAATGAGTATGT
10737 AGTTCAATGAGTATGT
1 AGTTCAATGAGTATGT
10753 A
1 A
10754 TTGAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
AGTTCAATGAGTATGT
Found at i:20564 original size:21 final size:21
Alignment explanation
Indices: 20534--20574 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20524 ACTTTTAGCA
20534 GACACATGAATCAACTTAATC
1 GACACATGAATCAACTTAATC
* * *
20555 GACACCTGAATTACCTTAAT
1 GACACATGAATCAACTTAAT
20575 TGGACAAATA
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:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (21 bp):
GACACATGAATCAACTTAATC
Found at i:23425 original size:4 final size:4
Alignment explanation
Indices: 23416--23474 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
23406 CTCTTATGTA
23416 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
23464 AAAT AAAT AAA
1 AAAT AAAT AAA
23475 AGACGATGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:23692 original size:26 final size:28
Alignment explanation
Indices: 23663--23715 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
23653 GTTTCGACAT
23663 CAGCTTAGT-C-GCCTATATATGCTATC
1 CAGCTTAGTCCAGCCTATATATGCTATC
23689 CAGCTTAGTCCATGCCTATATATGCTA
1 CAGCTTAGTCCA-GCCTATATATGCTA
23716 ACCATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.38
27 1 0.04
29 14 0.58
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (28 bp):
CAGCTTAGTCCAGCCTATATATGCTATC
Found at i:29030 original size:25 final size:25
Alignment explanation
Indices: 28996--29044 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28986 CCAAACAATC
28996 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
* *
29021 TTGAGCACTCTCGTTTGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
29045 CAAACCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.39
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:29070 original size:21 final size:21
Alignment explanation
Indices: 29041--29082 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29031 TCGTTTGGTC
*
29041 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
29061 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
29083 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:34793 original size:56 final size:56
Alignment explanation
Indices: 34668--34784 Score: 189
Period size: 56 Copynumber: 2.1 Consensus size: 56
34658 CCTTAACAAG
* * * *
34668 ACAACTTCCAGTGTTAAAAGATAATTTACCGTAGTAAATAAGTAATGTTTATTATG
1 ACAACATCCGGTGTTAAAAGATAATTTACCATAGTAAATAAGTAATGTTTATTATA
*
34724 ATAACATCCGGTGTTAAAAGATAATTTACCATAGTAAATAAGTAATGTTTATTATA
1 ACAACATCCGGTGTTAAAAGATAATTTACCATAGTAAATAAGTAATGTTTATTATA
34780 ACAAC
1 ACAAC
34785 TTTTGGTGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (56 bp):
ACAACATCCGGTGTTAAAAGATAATTTACCATAGTAAATAAGTAATGTTTATTATA
Found at i:34935 original size:41 final size:41
Alignment explanation
Indices: 34823--34975 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
34813 GTATTTCAAG
* **
34823 GTGACAACTTTTGGTGTCAATA--TAATTATAATTTACCGGA
1 GTGACAACTTTTGGTGTC-ATAGGTAATTTTAATTTACCAAA
* * * *
34863 GTGAC-ACTTTTGGTGTCAAATGTACTATTAATTTACCAAA
1 GTGACAACTTTTGGTGTCATAGGTAATTTTAATTTACCAAA
34903 GTGACAACTTTTGGTGTCATAGGTAATTTTAATTTACCAAA
1 GTGACAACTTTTGGTGTCATAGGTAATTTTAATTTACCAAA
* *
34944 GTGACAACTTCTGGTATCA-ATGGTAATTTTAA
1 GTGACAACTTTTGGTGTCATA-GGTAATTTTAA
34976 ATAATATCTA
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.02
39 12 0.12
40 24 0.25
41 59 0.61
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (41 bp):
GTGACAACTTTTGGTGTCATAGGTAATTTTAATTTACCAAA
Found at i:35774 original size:2 final size:2
Alignment explanation
Indices: 35767--35812 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
35757 GACCCTTTTA
35767 AT AT AT AT AT AT AT -T AT AT -T AT -T AT -T AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35803 AT AT AT AT AT
1 AT AT AT AT AT
35813 TTCCGTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
1 6 0.16
2 32 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:35792 original size:11 final size:13
Alignment explanation
Indices: 35768--35812 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 13
35758 ACCCTTTTAA
35768 TATATATATATAT
1 TATATATATATAT
35781 TATAT-TAT-TAT
1 TATATATATATAT
35792 TAT-TA-ATATA-
1 TATATATATATAT
35802 TATATATATAT
1 TATATATATAT
35813 TTCCGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 6 0.21
11 10 0.36
12 7 0.25
13 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATATATATAT
Found at i:36082 original size:36 final size:36
Alignment explanation
Indices: 36037--36109 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
36027 GAAACCCCTT
*
36037 ATTCATCCTCATCATCTCCATCTTTCTTTTTCTCTC
1 ATTCATCCTCATCATCTCCATCTCTCTTTTTCTCTC
*
36073 ATTCTTCCTCATCATCTCCATCTCTCTTTTTCTCTC
1 ATTCATCCTCATCATCTCCATCTCTCTTTTTCTCTC
36109 A
1 A
36110 GACCTAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.14, C:0.37, G:0.00, T:0.49
Consensus pattern (36 bp):
ATTCATCCTCATCATCTCCATCTCTCTTTTTCTCTC
Found at i:43986 original size:2 final size:2
Alignment explanation
Indices: 43979--44012 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
43969 TAATTTCCAC
43979 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
44013 CCTATCCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45169 original size:3 final size:3
Alignment explanation
Indices: 45161--45196 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
45151 CTAGTTATAG
45161 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
45197 GACGGAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:48752 original size:2 final size:2
Alignment explanation
Indices: 48745--48779 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48735 CATCAAACCC
48745 TA TA TA 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 TA TA TA T
48780 TTAAGCGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50380 original size:9 final size:9
Alignment explanation
Indices: 50366--50394 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
50356 TCTGAATATC
50366 ATATATCAT
1 ATATATCAT
50375 ATATATCAT
1 ATATATCAT
50384 ATATAT-AT
1 ATATATCAT
50392 ATA
1 ATA
50395 ATGATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATCAT
Found at i:51034 original size:2 final size:2
Alignment explanation
Indices: 51027--51118 Score: 125
Period size: 2 Copynumber: 44.5 Consensus size: 2
51017 AAATATAATC
51027 AT AT AT AT CAT AT CAT AT CAT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
51069 AT AT A- AT AT AT AT AT AT AT AT AT CAT AT AT CAT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT
51112 AT AT AT A
1 AT AT AT A
51119 ATGATAACAA
Statistics
Matches: 83, Mismatches: 0, Indels: 14
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.02
2 71 0.86
3 10 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:51092 original size:47 final size:50
Alignment explanation
Indices: 51019--51118 Score: 163
Period size: 47 Copynumber: 2.1 Consensus size: 50
51009 ATTTATAAAA
51019 ATATAATCATATATATCATATCATATCATATAAT-ATATATATATATATAT
1 ATATAATCATATATATCATATCATATCATAT-ATCATATATATATATATAT
51069 ATATAAT-ATATATAT-ATAT-ATATCATATATCATATATATATATATAT
1 ATATAATCATATATATCATATCATATCATATATCATATATATATATATAT
51116 ATA
1 ATA
51119 ATGATAACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
46 2 0.04
47 28 0.57
48 4 0.08
49 8 0.16
50 7 0.14
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (50 bp):
ATATAATCATATATATCATATCATATCATATATCATATATATATATATAT
Found at i:51132 original size:59 final size:55
Alignment explanation
Indices: 51018--51119 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 55
51008 AATTTATAAA
*
51018 AATATAATCATATATATCATATCATATCATATAATATATATATATATATATATAT
1 AATATAATCATATATATCATATCATATCATATAATATATATATATATATAAATAT
51073 AATAT-AT-ATATATAT-ATATCATAT-ATCAT-ATATATATATATATATAA
1 AATATAATCATATATATCATATCATATCAT-ATAATATATATATATATATAA
51120 TGATAACAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
51 19 0.42
52 11 0.24
53 8 0.18
54 2 0.04
55 5 0.11
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (55 bp):
AATATAATCATATATATCATATCATATCATATAATATATATATATATATAAATAT
Found at i:52925 original size:12 final size:13
Alignment explanation
Indices: 52902--52930 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52892 TAAGTTTGGT
52902 TTCTCTCTTCTTC
1 TTCTCTCTTCTTC
52915 TTCTC-CTTCTTC
1 TTCTCTCTTCTTC
52927 TTCT
1 TTCT
52931 TTCGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCTCTTCTTC
Done.