Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013043.1 Corchorus capsularis cultivar CVL-1 contig13064, 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: 31510
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:231 original size:17 final size:19
Alignment explanation
Indices: 197--233 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
187 CTACGTACTT
197 TTTATAATAAAAAGATATA
1 TTTATAATAAAAAGATATA
216 TTTAT-ATAAAAA-ATATA
1 TTTATAATAAAAAGATATA
233 T
1 T
234 AGTCGCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTATAATAAAAAGATATA
Found at i:3467 original size:27 final size:27
Alignment explanation
Indices: 3436--3489 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3426 TAATATACTC
3436 TTCCTTCCGCTCTTGGGTAAAACGGTT
1 TTCCTTCCGCTCTTGGGTAAAACGGTT
* *
3463 TTCCTTGCTCTCTTGGGTAAAACGGTT
1 TTCCTTCCGCTCTTGGGTAAAACGGTT
3490 GTGATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (27 bp):
TTCCTTCCGCTCTTGGGTAAAACGGTT
Found at i:5011 original size:12 final size:12
Alignment explanation
Indices: 4996--5021 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4986 AAAAAAATTG
4996 AACATGAAACCT
1 AACATGAAACCT
5008 AACATGAAACCT
1 AACATGAAACCT
5020 AA
1 AA
5022 AATAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (12 bp):
AACATGAAACCT
Found at i:11591 original size:3 final size:3
Alignment explanation
Indices: 11583--11620 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11573 AACTCAATTA
11583 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11621 CCTCTCACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13000 original size:37 final size:37
Alignment explanation
Indices: 12950--13023 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
12940 TCTTTCTAAG
12950 CCCCAAGTCAGCCTGTCATTAGATAAAAAAATGGGAA
1 CCCCAAGTCAGCCTGTCATTAGATAAAAAAATGGGAA
*
12987 CCCCAAGTCAGCCTGTCATTAGATAAAAAAATTGGAA
1 CCCCAAGTCAGCCTGTCATTAGATAAAAAAATGGGAA
13024 TAGGATGACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (37 bp):
CCCCAAGTCAGCCTGTCATTAGATAAAAAAATGGGAA
Found at i:13613 original size:76 final size:76
Alignment explanation
Indices: 13487--13640 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
13477 AAGTTTTCCA
13487 ATTAACATAGGGGATTTTGTCAGTATCTTTAGAATTGTTCCAAAGAAACTTCCTAAGTAAGGTGT
1 ATTAACATAGGGGATTTTGTCAGTATCTTTAGAATTGTTCCAAAGAAACTTCCTAAGTAAGGTGT
13552 TAATATTCTTG
66 TAATATTCTTG
13563 ATTAACATAGGGGATTTTGTCAGTATCTTTAGAATTGTTCCAAAGAAACTTCCTAAGTAAGGTGT
1 ATTAACATAGGGGATTTTGTCAGTATCTTTAGAATTGTTCCAAAGAAACTTCCTAAGTAAGGTGT
13628 TAATATTCTTG
66 TAATATTCTTG
13639 AT
1 AT
13641 AAAACATTTA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (76 bp):
ATTAACATAGGGGATTTTGTCAGTATCTTTAGAATTGTTCCAAAGAAACTTCCTAAGTAAGGTGT
TAATATTCTTG
Found at i:20867 original size:3 final size:3
Alignment explanation
Indices: 20861--20967 Score: 81
Period size: 3 Copynumber: 35.7 Consensus size: 3
20851 CTACAACGTG
* * * * * *
20861 CTT CTT CTT CTT CTT CTT CAT CAT CAT CTT CTT CTT CTT CAT CAT CAT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * *
20909 CTT CTT CTT CTT CTT CCT CTC CTG CTT CCTG C-G CTT CTT CAT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT
*
20954 CTT CTG CTT CTT CT
1 CTT CTT CTT CTT CT
20968 CCTTTATTTG
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.02
3 83 0.95
4 2 0.02
ACGTcount: A:0.07, C:0.36, G:0.04, T:0.53
Consensus pattern (3 bp):
CTT
Found at i:20892 original size:21 final size:21
Alignment explanation
Indices: 20866--20921 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
20856 ACGTGCTTCT
20866 TCTTCTTCTTCTTCATCATCA
1 TCTTCTTCTTCTTCATCATCA
20887 TCTTCTTCTTCTTCATCATCA
1 TCTTCTTCTTCTTCATCATCA
20908 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
20922 TTCCTCTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.11, C:0.34, G:0.00, T:0.55
Consensus pattern (21 bp):
TCTTCTTCTTCTTCATCATCA
Found at i:20966 original size:21 final size:21
Alignment explanation
Indices: 20863--20967 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
20853 ACAACGTGCT
*
20863 TCTTCTTCTTCTTCTTCATCA
1 TCTTCTTCTTCTTCTTCTTCA
* *
20884 TCATCTTCTTCTTCTTCATCA
1 TCTTCTTCTTCTTCTTCTTCA
* *
20905 TCATCTTCTTCTTCTTCTTCC
1 TCTTCTTCTTCTTCTTCTTCA
* * *
20926 TCTCCTGCTTCCTGCGCTTCTTCA
1 TCTTCTTCTT-CT--TCTTCTTCA
*
20950 TCTTCTTCTGCTTCTTCT
1 TCTTCTTCTTCTTCTTCT
20968 CCTTTATTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 51 0.74
22 2 0.03
23 2 0.03
24 14 0.20
ACGTcount: A:0.07, C:0.36, G:0.04, T:0.53
Consensus pattern (21 bp):
TCTTCTTCTTCTTCTTCTTCA
Found at i:21825 original size:21 final size:21
Alignment explanation
Indices: 21800--21862 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
21790 TGCAGGGTTT
21800 AATTTTCTCAAATTAGAGAGA
1 AATTTTCTCAAATTAGAGAGA
21821 AATTTTCTCAAATTAGAGAG-
1 AATTTTCTCAAATTAGAGAGA
* *
21841 -ATTTTCTGAAATAAGAGAGA
1 AATTTTCTCAAATTAGAGAGA
21861 AA
1 AA
21863 ACAAGACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.45
21 21 0.55
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (21 bp):
AATTTTCTCAAATTAGAGAGA
Found at i:24594 original size:55 final size:55
Alignment explanation
Indices: 24511--24623 Score: 183
Period size: 56 Copynumber: 2.1 Consensus size: 55
24501 AACACATTTC
*
24511 AATTTTTACCCTAACCAAGAATTTCTTACT-CAAAAAACCAAAAGAAAAAGGGAG
1 AATTTTTACCATAACCAAGAATTTCTTACTCCAAAAAACCAAAAGAAAAAGGGAG
* *
24565 AATTTTTCACCATCACCAAGAATTTCTTACTCCAAAAGACCAAAAGAAAAAGGGAG
1 AATTTTT-ACCATAACCAAGAATTTCTTACTCCAAAAAACCAAAAGAAAAAGGGAG
24621 AAT
1 AAT
24624 ATTAAGCATG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 7 0.13
55 21 0.39
56 26 0.48
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (55 bp):
AATTTTTACCATAACCAAGAATTTCTTACTCCAAAAAACCAAAAGAAAAAGGGAG
Found at i:24973 original size:2 final size:2
Alignment explanation
Indices: 24966--25014 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
24956 CTAAAACGTA
* *
24966 AT AT AT AT AT TT AT AT -T AT TT AT AT -T AT AT AT 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
25005 AT -T AT AT AT A
1 AT AT AT AT AT A
25015 AAATGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:25005 original size:16 final size:16
Alignment explanation
Indices: 24968--25015 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
24958 AAAACGTAAT
*
24968 ATATATATT-TATATT
1 ATATATATTATATATA
*
24983 ATTTATATTATATATA
1 ATATATATTATATATA
24999 ATATATATTATATATA
1 ATATATATTATATATA
25015 A
1 A
25016 AATGAAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATATTATATATA
Found at i:25513 original size:46 final size:46
Alignment explanation
Indices: 25457--25549 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
25447 TAATCTTATC
*
25457 TCTATTTTTTTTTACAAATCTCTACTCTTTATCAAGCTTTATAATA
1 TCTATTTTTTTCTACAAATCTCTACTCTTTATCAAGCTTTATAATA
25503 TCTATTTTTTTCTACAAATCTCTACTCTTTATCAAGCTTTATAATA
1 TCTATTTTTTTCTACAAATCTCTACTCTTTATCAAGCTTTATAATA
25549 T
1 T
25550 TAGACAAACT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (46 bp):
TCTATTTTTTTCTACAAATCTCTACTCTTTATCAAGCTTTATAATA
Found at i:27788 original size:49 final size:49
Alignment explanation
Indices: 27713--27821 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 49
27703 CCAATACTTA
* **
27713 AAAATCCAATAGAAAAGAGATAGTAAATGTATAAATTGCAAATAACAATC
1 AAAAT-CATTAGAAAAGAGATAGTAAATGTATAAATTAAAAATAACAATC
*
27763 AAAATCATTAGAAAAGAGATTGTAAATGTATAAATTAAAAATAACAATC
1 AAAATCATTAGAAAAGAGATAGTAAATGTATAAATTAAAAATAACAATC
27812 AAAATCATTA
1 AAAATCATTA
27822 TATTAATATT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
49 50 0.91
50 5 0.09
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (49 bp):
AAAATCATTAGAAAAGAGATAGTAAATGTATAAATTAAAAATAACAATC
Found at i:28090 original size:2 final size:2
Alignment explanation
Indices: 28083--28108 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28073 ATAATACAAA
28083 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28109 GTTGATGACT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28954 original size:50 final size:49
Alignment explanation
Indices: 28856--29137 Score: 327
Period size: 49 Copynumber: 5.7 Consensus size: 49
28846 AAAATGAACT
* * ** * *
28856 TGCCTTTCGTCCGGAAAGGGCACTTTGGGAAATGGCAGGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAA
* *
28905 CGCCTTCCGTCCGGGAAGGGCGTTTTTGGAAAATAGCAAGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCG-TTTTGGGAAATAGCAAGTAAAAATAAA
*
28955 TGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAA
* * * *
29004 TGGCTTCCGTCTGGAAAGGGCGTTTTGGGAAATAG---GTAAAGATTATTGAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAA-A--A-TAAA
* *
29054 TGCCTTCCGCCCGGGAAGGGTGTTTTGGGAAATAGCAAGTAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAA
* * * *
29103 TGGCTTCCGTCTGAGAAGGGCGTTTGGGGAAATAG
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAG
29138 GGAAAGATTG
Statistics
Matches: 199, Mismatches: 26, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
46 5 0.03
47 1 0.01
49 110 0.55
50 77 0.39
52 1 0.01
53 5 0.03
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (49 bp):
TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAA
Found at i:28974 original size:99 final size:99
Alignment explanation
Indices: 28856--29178 Score: 347
Period size: 99 Copynumber: 3.3 Consensus size: 99
28846 AAAATGAACT
* * ** * * * * *
28856 TGCCTTTCGTCCGGAAAGGGCACTTTGGGAAATGGCAGGTAAAAATAAACGCCTTCCGTCCGGGA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGA
28921 AGGGCGTTTTTGGAAAATAGCAAGTAAA-A-A-TAAA
66 AGGGCGTTTTTGGAAAATAG---GTAAAGATATTAAA
* *
28955 TGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGA
* *
29020 AGGGCG-TTTTGGGAAATAGGTAAAGATTATTGAA
66 AGGGCGTTTTTGGAAAATAGGTAAAGA-TATTAAA
* * *
29054 TGCCTTCCGCCCGGGAAGGGTGTTTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGAGA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGA
* * * *
29119 AGGGCG-TTTGGGGAAATAGGGAAAG--ATT-GA
66 AGGGCGTTTTTGGAAAATAGGTAAAGATATTAAA
* * *
29149 TACCTTCCGTCTGGGAAGGACGTTTTGGGA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGA
29179 TAAAGTTTGA
Statistics
Matches: 194, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
95 31 0.16
96 4 0.02
98 13 0.07
99 146 0.75
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (99 bp):
TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGA
AGGGCGTTTTTGGAAAATAGGTAAAGATATTAAA
Done.