Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012204.1 Corchorus capsularis cultivar CVL-1 contig12225, 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: 68851
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6938 original size:1 final size:1
Alignment explanation
Indices: 6932--6959 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
6922 GGACTTAAAT
6932 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
6960 CCTTCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8471 original size:12 final size:12
Alignment explanation
Indices: 8454--8524 Score: 88
Period size: 12 Copynumber: 5.9 Consensus size: 12
8444 GCTCGACTCG
**
8454 TCCTCCTCTTGA
1 TCCTCCTCTTCC
*
8466 TCCTCCTCGTCC
1 TCCTCCTCTTCC
8478 TCCTCCTCTTCC
1 TCCTCCTCTTCC
* *
8490 TCCTCCCCTTTC
1 TCCTCCTCTTCC
8502 TCCTCCTCTTCC
1 TCCTCCTCTTCC
*
8514 TTCTCCTCTTC
1 TCCTCCTCTTC
8525 TTCGTAGTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.01, C:0.54, G:0.03, T:0.42
Consensus pattern (12 bp):
TCCTCCTCTTCC
Found at i:8472 original size:3 final size:3
Alignment explanation
Indices: 8466--8521 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
8456 CTCCTCTTGA
* * * *
8466 TCC TCC TCG TCC TCC TCC TCT TCC TCC TCC -CC TTTC TCC TCC TCT
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC -TCC TCC TCC TCC
*
8511 TCC TTC TCC TC
1 TCC TCC TCC TC
8522 TTCTTCGTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.93
4 1 0.02
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.41
Consensus pattern (3 bp):
TCC
Found at i:10456 original size:2 final size:2
Alignment explanation
Indices: 10449--10479 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10439 TGCCATGGAT
10449 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 T
10480 CCCTTCCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11126 original size:13 final size:14
Alignment explanation
Indices: 11095--11126 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
11085 TCAAAATATA
11095 ATTTTTTAAAATTT
1 ATTTTTTAAAATTT
11109 ATTTTTTAAAATTT
1 ATTTTTTAAAATTT
11123 -TTTT
1 ATTTT
11127 ATAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTTAAAATTT
Found at i:15890 original size:8 final size:7
Alignment explanation
Indices: 15882--15933 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
15872 ATTCTTCTTC
15882 TCTTTTT
1 TCTTTTT
15889 CTCTCTTTT
1 -TCT-TTTT
15898 TCTTTTT
1 TCTTTTT
15905 T-TTTTT
1 TCTTTTT
*
15911 ACATTTTTT
1 TC--TTTTT
15920 TCTTTTT
1 TCTTTTT
15927 TCTTTTT
1 TCTTTTT
15934 AATTTTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 5 0.13
7 17 0.45
8 6 0.16
9 10 0.26
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (7 bp):
TCTTTTT
Found at i:15919 original size:22 final size:22
Alignment explanation
Indices: 15894--15939 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
15884 TTTTTCTCTC
15894 TTTTTCTTTTTT-TTTTTACATT
1 TTTTTCTTTTTTCTTTTTA-ATT
15916 TTTTTCTTTTTTCTTTTTAATT
1 TTTTTCTTTTTTCTTTTTAATT
15938 TT
1 TT
15940 CTTTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTCTTTTTTCTTTTTAATT
Found at i:15939 original size:29 final size:28
Alignment explanation
Indices: 15882--15946 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
15872 ATTCTTCTTC
* **
15882 TCTTTTTCTCTCTTTTTCTTTTTTTTTT
1 TCTTTTTTTCTCTTTTTCTTTTTAATTT
15910 TACATTTTTTTCT-TTTTTCTTTTTAATTT
1 T-C-TTTTTTTCTCTTTTTCTTTTTAATTT
15939 TCTTTTTT
1 TCTTTTTT
15947 CCTGTTCTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.19
28 2 0.06
29 16 0.50
30 8 0.25
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (28 bp):
TCTTTTTTTCTCTTTTTCTTTTTAATTT
Found at i:24396 original size:31 final size:31
Alignment explanation
Indices: 24360--24427 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
24350 ATGAGAATTC
* *
24360 AATTGACTCAATCTTGTGAGTAC-ATTGACTA
1 AATTGACTCAATCATGTGACTACAATT-ACTA
*
24391 AATTGACTCGATCATGTGACTACAATTACTA
1 AATTGACTCAATCATGTGACTACAATTACTA
24422 AATTGA
1 AATTGA
24428 TCGCTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (31 bp):
AATTGACTCAATCATGTGACTACAATTACTA
Found at i:27825 original size:1 final size:1
Alignment explanation
Indices: 27786--27810 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
27776 GATATTGGTG
27786 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
27811 AGAATATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:41245 original size:11 final size:11
Alignment explanation
Indices: 41214--41267 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 11
41204 TCTAACAAAT
41214 ATAATTCACAA
1 ATAATTCACAA
41225 A-AATTCACAA
1 ATAATTCACAA
*
41235 ATAATTAAC-A
1 ATAATTCACAA
* *
41245 ATTA-GCAC-A
1 ATAATTCACAA
41254 ATAATTCACAA
1 ATAATTCACAA
41265 ATA
1 ATA
41268 TAACACCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 6 0.18
10 17 0.50
11 11 0.32
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.26
Consensus pattern (11 bp):
ATAATTCACAA
Found at i:42019 original size:51 final size:50
Alignment explanation
Indices: 41938--42038 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
41928 ATAAGTAAAA
* * * *
41938 CAAAATCAATAAAAACAGTGACATAGTCTCAAATTAACATTGTTTTTAAG
1 CAAAACCAATAAAAACAATAACATAGTCTCAAATTAACATTGTTTCTAAG
* *
41988 CAAAACCAATAATAAACAATAACATTGTCTCAAGTTAACATTGTTTCTAAG
1 CAAAACCAATAA-AAACAATAACATAGTCTCAAATTAACATTGTTTCTAAG
42039 TTAGATAGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 11 0.25
51 33 0.75
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (50 bp):
CAAAACCAATAAAAACAATAACATAGTCTCAAATTAACATTGTTTCTAAG
Found at i:42028 original size:16 final size:17
Alignment explanation
Indices: 42007--42041 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41997 TAATAAACAA
42007 TAACATTGTCTC-AAGT
1 TAACATTGTCTCTAAGT
*
42023 TAACATTGTTTCTAAGT
1 TAACATTGTCTCTAAGT
42040 TA
1 TA
42042 GATAGCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
TAACATTGTCTCTAAGT
Found at i:42999 original size:86 final size:85
Alignment explanation
Indices: 42840--43008 Score: 221
Period size: 86 Copynumber: 2.0 Consensus size: 85
42830 CCCATCATCT
* * *
42840 CAAAGAAAAATACAGTGAATCAAAGCATTGAATGAAGAAATTAGGCAAAGAAACAACAGATTTAC
1 CAAACAAAAATACAGTGAATCAAAGCATTGAATAAAGAAATTAGGCAAAGAAACAACAGATTAAC
*
42905 TTGATTCGAACCCAAAAATA
66 TTCATTCGAACCCAAAAATA
* ** * * * **
42925 CAAACAAAAGTACAGTTTATCAAAGCATTGAATCAAAGAATTTGGGCAAATAAACAGTAGATTAA
1 CAAACAAAAATACAGTGAATCAAAGCATTGAAT-AAAGAAATTAGGCAAAGAAACAACAGATTAA
42990 CTTCATTCGAACCCAAAAA
65 CTTCATTCGAACCCAAAAA
43009 AATCAAACTC
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 29 0.41
86 42 0.59
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (85 bp):
CAAACAAAAATACAGTGAATCAAAGCATTGAATAAAGAAATTAGGCAAAGAAACAACAGATTAAC
TTCATTCGAACCCAAAAATA
Found at i:43146 original size:22 final size:22
Alignment explanation
Indices: 43120--43162 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
43110 ACCGTCAAAT
*
43120 AAACCCTCGAACCACCGGAAGC
1 AAACCCTCAAACCACCGGAAGC
43142 AAACCCTCAAACCACCGGAAG
1 AAACCCTCAAACCACCGGAAG
43163 TAAAGCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.16, T:0.05
Consensus pattern (22 bp):
AAACCCTCAAACCACCGGAAGC
Found at i:43286 original size:16 final size:16
Alignment explanation
Indices: 43265--43296 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43255 CAGAAAACTT
43265 CATTTTCATTTTATTA
1 CATTTTCATTTTATTA
43281 CATTTTCATTTTATTA
1 CATTTTCATTTTATTA
43297 TTTTACTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTTCATTTTATTA
Found at i:47046 original size:32 final size:33
Alignment explanation
Indices: 47005--47078 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 33
46995 AATTGATCTA
47005 GACGCCTCCCACCGTGATCGGGCGCCCTC-CGG
1 GACGCCTCCCACCGTGATCGGGCGCCCTCACGG
* * * *
47037 GACGCCTCCCACCGTGGTGGGGTGCCCTCAGGG
1 GACGCCTCCCACCGTGATCGGGCGCCCTCACGG
47070 GACGCCTCC
1 GACGCCTCC
47079 GTGTCTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 26 0.70
33 11 0.30
ACGTcount: A:0.09, C:0.43, G:0.34, T:0.14
Consensus pattern (33 bp):
GACGCCTCCCACCGTGATCGGGCGCCCTCACGG
Found at i:47253 original size:13 final size:13
Alignment explanation
Indices: 47235--47260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47225 TCAATAGTGG
47235 TGCTTAACCAATC
1 TGCTTAACCAATC
47248 TGCTTAACCAATC
1 TGCTTAACCAATC
47261 GTGTAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
TGCTTAACCAATC
Found at i:54076 original size:14 final size:14
Alignment explanation
Indices: 54057--54095 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
54047 ATACTACTAG
54057 AAACAAATACAAGC
1 AAACAAATACAAGC
54071 AAACAAATACAAGC
1 AAACAAATACAAGC
54085 AAACAAATACA
1 AAACAAATACA
54096 GCTTGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.08
Consensus pattern (14 bp):
AAACAAATACAAGC
Found at i:63990 original size:38 final size:38
Alignment explanation
Indices: 63948--64020 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
63938 GTGCATAGTG
* *
63948 GACCCGTGCCTCAGGGGGTTAAGCTGTTGGTAAGAGTA
1 GACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAGAGTA
63986 GACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAGA
1 GACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAGA
64021 TTATGATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.36, T:0.22
Consensus pattern (38 bp):
GACCCGTGCCTCAGGGGGTTAAACTGTTGGCAAGAGTA
Found at i:67142 original size:18 final size:19
Alignment explanation
Indices: 67105--67143 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
67095 TCTCTCTCTC
67105 TTGTCTATTTTCATTTTTT
1 TTGTCTATTTTCATTTTTT
67124 TTGTCTATTTTCATTTTTT
1 TTGTCTATTTTCATTTTTT
67143 T
1 T
67144 AGTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (19 bp):
TTGTCTATTTTCATTTTTT
Found at i:67149 original size:17 final size:18
Alignment explanation
Indices: 67109--67150 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
67099 TCTCTCTTGT
*
67109 CTATTTTCATTTTTTTTG
1 CTATTTTCATTTTTTTAG
67127 TCTATTTTCATTTTTTTAG
1 -CTATTTTCATTTTTTTAG
67146 -TATTT
1 CTATTT
67151 ATTAAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
19 17 0.77
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (18 bp):
CTATTTTCATTTTTTTAG
Found at i:68291 original size:34 final size:33
Alignment explanation
Indices: 68253--68390 Score: 201
Period size: 34 Copynumber: 4.2 Consensus size: 33
68243 TAACCCGTTA
68253 GCAGGTTCTTCCAGTTATTATCACAACCCACTGG
1 GCAGG-TCTTCCAGTTATTATCACAACCCACTGG
*
68287 GCAGGATCTTCCAGTTATTTTCACAACCCACTGG
1 GCAGG-TCTTCCAGTTATTATCACAACCCACTGG
*
68321 GTAGGGTCTTCCAGTTATTATCACAACCCACTGG
1 GCA-GGTCTTCCAGTTATTATCACAACCCACTGG
68355 GCAGAGTCTTCCAGTTATTAT---AACCCACTGG
1 GCAG-GTCTTCCAGTTATTATCACAACCCACTGG
68386 GCAGG
1 GCAGG
68391 GCCGATGAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
30 1 0.01
31 14 0.14
33 1 0.01
34 79 0.81
35 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (33 bp):
GCAGGTCTTCCAGTTATTATCACAACCCACTGG
Found at i:68750 original size:22 final size:20
Alignment explanation
Indices: 68730--68767 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
68720 CTCCAACTAA
68730 AACACGGCCTTTCACCAACT
1 AACACGGCCTTTCACCAACT
* *
68750 AATACGGCCTTTCCCCAA
1 AACACGGCCTTTCACCAA
68768 GTACTTAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.39, G:0.11, T:0.21
Consensus pattern (20 bp):
AACACGGCCTTTCACCAACT
Done.