Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020422.1 Corchorus olitorius cultivar O-4 contig20455, 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: 27804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA 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 TA T
38 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42 original size:2 final size:2
Alignment explanation
Indices: 37--87 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
27 TATATATATA
37 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
79 TG TG TG TG T
1 TG TG TG TG T
88 CTTTGACTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1079 original size:6 final size:6
Alignment explanation
Indices: 1068--1092 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1058 CTAGTTCAAT
1068 TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA T
1093 ATTAGTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (6 bp):
TCCAAA
Found at i:7925 original size:40 final size:40
Alignment explanation
Indices: 7862--7947 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
7852 GTCCGCCTCG
* * *
7862 TTATCTCTAATTGGCTCTATGCAACAACTAAGCTCCGTGC
1 TTATCTCAAATTGGCTCCATGCAACAACTAAGCTCCGTCC
* *
7902 TTATCTCAAATTTGCTCCGTGCAACAACTAAGCTCCGTCC
1 TTATCTCAAATTGGCTCCATGCAACAACTAAGCTCCGTCC
7942 TTATCT
1 TTATCT
7948 TATTTCAGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (40 bp):
TTATCTCAAATTGGCTCCATGCAACAACTAAGCTCCGTCC
Found at i:8755 original size:22 final size:22
Alignment explanation
Indices: 8738--9005 Score: 131
Period size: 22 Copynumber: 12.2 Consensus size: 22
8728 TAAAATTTAA
8738 ATAACCACCTAATGAAATTTTG
1 ATAACCACCTAATGAAATTTTG
8760 ATAACCACCCT-ATGAAATTTTG
1 ATAACCA-CCTAATGAAATTTTG
* * *
8782 ATAACCTCCCAATGAAATGTTG
1 ATAACCACCTAATGAAATTTTG
* * *
8804 GTAAGCACACATTATGAAATTTTG
1 ATAA-C-CACCTAATGAAATTTTG
* ** * *
8828 AAAACCTTCTGATGAAATATTG
1 ATAACCACCTAATGAAATTTTG
* * * * *
8850 GTAATCACATTATAAAATTTTG
1 ATAACCACCTAATGAAATTTTG
*** * *
8872 ATAACCGTATCATGAAATTGTG
1 ATAACCACCTAATGAAATTTTG
8894 AT-ACCTTA-CT-ATGAAAATTTT-
1 ATAACC--ACCTAATG-AAATTTTG
* * *
8915 ATAAACCTCCTTATAAAATTTTG
1 AT-AACCACCTAATGAAATTTTG
* *
8938 ATAACCTCC-ATTTGAAATTTTG
1 ATAACCACCTA-ATGAAATTTTG
*
8960 AT-A--ACCTCATGAAATTTTG
1 ATAACCACCTAATGAAATTTTG
* * *
8979 ATAACCATCTTATAAAATTTTG
1 ATAACCACCTAATGAAATTTTG
9001 ATAAC
1 ATAAC
9006 ATACCTATAA
Statistics
Matches: 183, Mismatches: 46, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
19 14 0.08
20 1 0.01
21 11 0.06
22 131 0.72
23 12 0.07
24 14 0.08
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
ATAACCACCTAATGAAATTTTG
Found at i:8929 original size:66 final size:62
Alignment explanation
Indices: 8859--9005 Score: 167
Period size: 66 Copynumber: 2.3 Consensus size: 62
8849 GGTAATCACA
8859 TTATAAAATTTTGATAACCGT-ATCATGAAATTGTGAT-ACCTTACTATGAAAATTTT-ATAAAC
1 TTATAAAATTTTGATAACC-TCAT-ATGAAATTGTGATAACC-T-C-ATG-AAATTTTGAT-AAC
8921 C-TCC
59 CAT-C
* *
8925 TTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTCATGAAATTTTGATAACCATC
1 TTATAAAATTTTGATAACCT-CATATGAAATTGTGATAACCTCATGAAATTTTGATAACCATC
8988 TTATAAAATTTTGATAAC
1 TTATAAAATTTTGATAAC
9006 ATACCTATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
63 30 0.41
64 6 0.08
65 2 0.03
66 31 0.42
67 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (62 bp):
TTATAAAATTTTGATAACCTCATATGAAATTGTGATAACCTCATGAAATTTTGATAACCATC
Found at i:9014 original size:22 final size:22
Alignment explanation
Indices: 8593--9055 Score: 115
Period size: 22 Copynumber: 21.1 Consensus size: 22
8583 TTGATAATCA
* *
8593 CTATAAAATTTTAATAACCT-C
1 CTATAAAATTTTGATAACATAC
*
8614 CATATAAAATTTTGATAA-TTAC
1 C-TATAAAATTTTGATAACATAC
* * *
8636 ACCATAAAGTTCTT-ATGACGATA-
1 -CTATAAAATT-TTGATAAC-ATAC
* * *
8659 CTATAAAATTTCGAGAACCT-C
1 CTATAAAATTTTGATAACATAC
* * * *
8680 CATATAAAATTGTGTTAACTTCC
1 C-TATAAAATTTTGATAACATAC
*
8703 CTATAAAATTTTG-TTACACTAC
1 CTATAAAATTTTGATAACA-TAC
** *
8725 CTATAAAATTTAAATAAC-CAC
1 CTATAAAATTTTGATAACATAC
* *
8746 CTAATGAAATTTTGATAACCA-CC
1 CT-ATAAAATTTTGATAA-CATAC
* * *
8769 CTATGAAATTTTGATAACCTCC
1 CTATAAAATTTTGATAACATAC
* * * * *
8791 CAATGAAATGTTGGTAAGCACAC
1 CTATAAAATTTTGATAA-CATAC
* * * * *
8814 ATTATGAAATTTTGAAAACCT-T
1 -CTATAAAATTTTGATAACATAC
* * * *
8836 CTGATGAAATATTGGTAATCACA-
1 CT-ATAAAATTTTGATAA-CATAC
* * *
8859 TTATAAAATTTTGATAACCGTAT
1 CTATAAAATTTTGATAA-CATAC
* * * *
8882 C-ATGAAATTGTGATACCTTA-
1 CTATAAAATTTTGATAACATAC
*
8902 CTATGAAAATTTT-ATAAACCT-C
1 CTAT-AAAATTTTGAT-AACATAC
*
8924 CTTATAAAATTTTGATAACCT-C
1 C-TATAAAATTTTGATAACATAC
* * *
8946 CATTTGAAATTTTGATAACCT--
1 C-TATAAAATTTTGATAACATAC
*
8967 C-ATGAAATTTTGATAACCAT-C
1 CTATAAAATTTTGATAA-CATAC
*
8988 TTATAAAATTTTGATAACATAC
1 CTATAAAATTTTGATAACATAC
* *
9010 CTAT-AAATTTTCTATAAC-TTC
1 CTATAAAATTTT-GATAACATAC
*
9031 CTTATAAAATTTTGTTAACAT-C
1 C-TATAAAATTTTGATAACATAC
9053 CTA
1 CTA
9056 GAGAATTCCA
Statistics
Matches: 328, Mismatches: 78, Indels: 72
0.69 0.16 0.15
Matches are distributed among these distances:
19 14 0.04
20 3 0.01
21 37 0.11
22 230 0.70
23 30 0.09
24 14 0.04
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
CTATAAAATTTTGATAACATAC
Found at i:9027 original size:63 final size:63
Alignment explanation
Indices: 8859--9020 Score: 158
Period size: 63 Copynumber: 2.5 Consensus size: 63
8849 GGTAATCACA
* *
8859 TTATAAAATTTTGATAAC--CGTATCATGAAATTGTGAT-ACCTTACTATGAAAATTTTATAAAC
1 TTATAAAATTTTGATAACATC-CAT-ATGAAATTTTGATAACC-T-C-ATG-AAATTTTATAAAC
8921 CTCC
60 CTCC
* *
8925 TTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAACCTCATGAAATTTTGAT-AACCAT-C
1 TTATAAAATTTTGATAACATCCATATGAAATTTTGATAACCTCATGAAATTTT-ATAAACC-TCC
8988 TTATAAAATTTTGATAACATACC-TAT-AAATTTT
1 TTATAAAATTTTGATAACAT-CCATATGAAATTTT
9021 CTATAACTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
62 7 0.08
63 33 0.39
64 8 0.09
65 1 0.01
66 30 0.35
67 5 0.06
68 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (63 bp):
TTATAAAATTTTGATAACATCCATATGAAATTTTGATAACCTCATGAAATTTTATAAACCTCC
Found at i:14065 original size:2 final size:2
Alignment explanation
Indices: 14058--14098 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14048 CTGTAGTTGA
14058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14099 GTGGGTAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19401 original size:36 final size:36
Alignment explanation
Indices: 19361--19444 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
19351 GGAAGTGATA
*
19361 GTTATGGAGGTGGCCAGGCTAAATCAGGAGATTATG
1 GTTATGGAGGTGGCCAGACTAAATCAGGAGATTATG
* *
19397 GTTATGGA-GTCAGCCAGACTAAGTCAGGAGATTATG
1 GTTATGGAGGT-GGCCAGACTAAATCAGGAGATTATG
*
19433 GCTATGGAGGTG
1 GTTATGGAGGTG
19445 ATGGTTATGG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.05
36 37 0.90
37 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.36, T:0.25
Consensus pattern (36 bp):
GTTATGGAGGTGGCCAGACTAAATCAGGAGATTATG
Found at i:19650 original size:102 final size:102
Alignment explanation
Indices: 19524--19776 Score: 331
Period size: 102 Copynumber: 2.5 Consensus size: 102
19514 AGAGACAACC
19524 TGCATCCGCTTACTCTAGTGGTAATGTACTGGGGGGTGGTTATGGTTATGGAAGTGATGGTTATG
1 TGCATCCGCTTACTCTAGTGGTAATGTACT-GGGGGTGGTTATGGTTATGGAAGTGATGGTTATG
* *
19589 G-AGGCAG-CCAGGCTAAATCAGATGATTACAGGAAGGA
65 GAAGG-AGACCAGACTAAATCAGAAGATTACAGGAAGGA
* *
19626 TGCATCCGCTTATTCTAGTGGTAATGCCAC---GGGTGGTTATGGTTATGGAAGTGATGGTTATG
1 TGCATCCGCTTACTCTAGTGGTAATG-TACTGGGGGTGGTTATGGTTATGGAAGTGATGGTTATG
* * *
19688 GATCAGGTGACCAGACTAAATCCGAAGATTACCGGAAGGA
65 GA--AGGAGACCAGACTAAATCAGAAGATTACAGGAAGGA
* *
19728 TGCATCCGCTTACTCTAGTGGTAATTTA--GGCGGTGGTTATGGTTATGGA
1 TGCATCCGCTTACTCTAGTGGTAATGTACTGGGGGTGGTTATGGTTATGGA
19777 GGTGGCCAGG
Statistics
Matches: 133, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
99 33 0.25
101 2 0.02
102 96 0.72
103 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (102 bp):
TGCATCCGCTTACTCTAGTGGTAATGTACTGGGGGTGGTTATGGTTATGGAAGTGATGGTTATGG
AAGGAGACCAGACTAAATCAGAAGATTACAGGAAGGA
Found at i:24905 original size:1 final size:1
Alignment explanation
Indices: 24899--24929 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
24889 CTTCTCATCA
24899 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24930 CTAGAGATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.