Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008276.1 Corchorus capsularis cultivar CVL-1 contig08297, 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: 46274
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4529 original size:27 final size:28
Alignment explanation
Indices: 4489--4557 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
4479 GTCTAAGGGT
4489 ATTTTGGTCA-TTTTTGCACCCAGGGGC
1 ATTTTGGTCATTTTTTGCACCCAGGGGC
*
4516 A-TTTGGTCATTTTTTGCACTCAGGGGC
1 ATTTTGGTCATTTTTTGCACCCAGGGGC
*
4543 ATTTTAGTCATTTTT
1 ATTTTGGTCATTTTT
4558 AGGTTCACCT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 8 0.21
27 18 0.47
28 12 0.32
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (28 bp):
ATTTTGGTCATTTTTTGCACCCAGGGGC
Found at i:7262 original size:29 final size:30
Alignment explanation
Indices: 7190--7262 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
7180 GACATGTCCG
*
7190 GGGGCATATTGGCACAATTTTAATAGTTGAA
1 GGGGCAAATTGGCACAA-TTTAATAGTTGAA
* * * *
7221 GGGG-TAATGTGGCACAA-TTATTAGTTTAT
1 GGGGCAAAT-TGGCACAATTTAATAGTTGAA
7250 GGGGCAAATTGGC
1 GGGGCAAATTGGC
7263 TTAAATTTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
29 17 0.50
30 5 0.15
31 12 0.35
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.32
Consensus pattern (30 bp):
GGGGCAAATTGGCACAATTTAATAGTTGAA
Found at i:18719 original size:20 final size:19
Alignment explanation
Indices: 18694--18758 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
18684 AATGCAACAC
18694 TATTAAATAAACATAATACA
1 TATT-AATAAACATAATACA
*
18714 TATTAATAATACAGATATCACA
1 TATTAATAA-ACATA-AT-ACA
* *
18736 TTATTAATAAAGATAATATA
1 -TATTAATAAACATAATACA
18756 TAT
1 TAT
18759 ATATATATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
19 8 0.22
20 10 0.27
21 4 0.11
22 6 0.16
23 9 0.24
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (19 bp):
TATTAATAAACATAATACA
Found at i:21149 original size:31 final size:30
Alignment explanation
Indices: 21114--21185 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
21104 ATACCGTACA
21114 GGTCCCTCTACTTACAAAAAGGGATCAATTT
1 GGTCCCTCTACTTACAAAAAGGG-TCAATTT
* * **
21145 GGTCCCACTAC-TATAAAAATTGTCAATTT
1 GGTCCCTCTACTTACAAAAAGGGTCAATTT
*
21174 GGTCCCTTTACT
1 GGTCCCTCTACT
21186 CATAATTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 16 0.47
30 8 0.24
31 10 0.29
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAGGGTCAATTT
Found at i:25844 original size:14 final size:16
Alignment explanation
Indices: 25820--25853 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
25810 CTATTGCTTT
25820 CTTTATAATCTG-TTG
1 CTTTATAATCTGTTTG
25835 CTTT-TAATCTGTTTG
1 CTTTATAATCTGTTTG
25850 CTTT
1 CTTT
25854 CTTAGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (16 bp):
CTTTATAATCTGTTTG
Found at i:26637 original size:20 final size:21
Alignment explanation
Indices: 26607--26648 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
26597 GTCATGTTAA
26607 GTTTATTTTTAATA-AGTAAAT
1 GTTTATTTTTAA-AGAGTAAAT
26628 GTTT-TTTTTAAAGAGTAAAT
1 GTTTATTTTTAAAGAGTAAAT
26648 G
1 G
26649 GGTTTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 15 0.75
21 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
GTTTATTTTTAAAGAGTAAAT
Found at i:27710 original size:13 final size:13
Alignment explanation
Indices: 27692--27721 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
27682 TTTAAATGTC
27692 TTTTAATTTTCTT
1 TTTTAATTTTCTT
27705 TTTTAATTTTCTT
1 TTTTAATTTTCTT
27718 TTTT
1 TTTT
27722 TCACTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTAATTTTCTT
Found at i:31088 original size:7 final size:6
Alignment explanation
Indices: 31079--31112 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
31069 CGTTTTCGTT
31079 TTTTTG TTTTTTG TTTTTG -TTTTG TTTTTG TTTT
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTT
31113 ACTTTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:31103 original size:11 final size:11
Alignment explanation
Indices: 31070--31137 Score: 68
Period size: 11 Copynumber: 6.3 Consensus size: 11
31060 GTTTGGCATC
*
31070 GTTTTCGTTTT
1 GTTTTTGTTTT
31081 -TTTGTT-TTTT
1 GTTT-TTGTTTT
31091 GTTTTTGTTTT
1 GTTTTTGTTTT
31102 GTTTTTGTTTT
1 GTTTTTGTTTT
**
31113 ACTTTTGTTTT
1 GTTTTTGTTTT
* *
31124 ATTTTTGTTAT
1 GTTTTTGTTTT
31135 GTT
1 GTT
31138 GTCAATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 9 0.19
11 39 0.81
ACGTcount: A:0.04, C:0.03, G:0.15, T:0.78
Consensus pattern (11 bp):
GTTTTTGTTTT
Found at i:33124 original size:18 final size:18
Alignment explanation
Indices: 33090--33124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33080 TGTTAAGGAA
*
33090 ATCTGAGAGATGGAAGAG
1 ATCTGAGAGATGAAAGAG
*
33108 ATCTGAGATATGAAAGA
1 ATCTGAGAGATGAAAGA
33125 AAAACCCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.31, T:0.20
Consensus pattern (18 bp):
ATCTGAGAGATGAAAGAG
Found at i:37195 original size:92 final size:91
Alignment explanation
Indices: 37058--37238 Score: 211
Period size: 92 Copynumber: 2.0 Consensus size: 91
37048 TTAACCAATA
* * * * * ** *
37058 AATCATGAATAAGGAAGAAGAAGGAAGTCTAAACTAGCAACAAAACTTTAGAATTCATAACCTAA
1 AATCATGAAGAAGGAAAAAGAAAGAAGTCTAAAATAGCAACAAAACTTCA-AACCCAGAACCTAA
* *
37123 GCAATCTATCAGCACGAAAAACCAAGG
65 ACAATATATCAGCACGAAAAACCAAGG
* *
37150 AATCATGAAGAATGAAAAAGAAAGAAG-CTTAAAATAGCATCAAAACTTCAAACCCAGAACCTAA
1 AATCATGAAGAAGGAAAAAGAAAGAAGTC-TAAAATAGCAACAAAACTTCAAACCCAGAACCTAA
* *
37214 ATAATATATCAGCACGGAAAACCAA
65 ACAATATATCAGCACGAAAAACCAA
37239 TGAGTCGATG
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
91 33 0.45
92 41 0.55
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (91 bp):
AATCATGAAGAAGGAAAAAGAAAGAAGTCTAAAATAGCAACAAAACTTCAAACCCAGAACCTAAA
CAATATATCAGCACGAAAAACCAAGG
Found at i:40579 original size:2 final size:2
Alignment explanation
Indices: 40572--40596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40562 ATTTGGTATC
40572 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 A
40597 CCATTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42311 original size:11 final size:9
Alignment explanation
Indices: 42285--42309 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42275 GTTAAAAATA
42285 ATATATAGT
1 ATATATAGT
42294 ATATATAGT
1 ATATATAGT
42303 ATATATA
1 ATATATA
42310 TAATCAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:42760 original size:19 final size:19
Alignment explanation
Indices: 42733--42771 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42723 TTCTTATATG
* *
42733 TAACTGTTTCACCACCGTT
1 TAACCGTTTCACAACCGTT
42752 TAACCGTTTCACAACCGTT
1 TAACCGTTTCACAACCGTT
42771 T
1 T
42772 TGGGTCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.36
Consensus pattern (19 bp):
TAACCGTTTCACAACCGTT
Found at i:43344 original size:200 final size:195
Alignment explanation
Indices: 42831--43769 Score: 1177
Period size: 200 Copynumber: 4.7 Consensus size: 195
42821 ATATTAAATA
*
42831 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATA
1 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATG
* * *
42896 GGGTATGTGTCAACTTCTTAACCCACTTATGAAGTTCAAAATTTATACTGATAGTGTATT-TATA
66 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATA
* * *
42960 ATAATCCTATAAGAAAAATTATGCAATACGCCGTCCGTGGAGTTTAGCAGACTGCACGTGCGGGG
131 ATAATCCTATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTACGGGG
* * * *
43025 TTTAACTTTAAGGGTTGAGATGTGTATCCTTAGGGAATATATATTAATGTTAAATATTTAATTAT
1 ------TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTAT
* *
43090 GAAATGGGGTATGTGTAAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTAT
60 GAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTAT
* *
43155 TGTATAATAATCCTATAAGAAAAATTATGCAATACACCATTAGTGGAGTTTAGCAGACTGCACGT
125 TGTATAATAATCCTATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGT
*
43220 GCGGGG
190 ACGGGG
*
43226 TTTAACTTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTGATTAT
1 ------TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTAT
* * *
43291 GAAATGGGATATGTGTCAACTT-TTAACCCGCTTATGGAATCCAAAATTTATACTGACAGTGTAT
60 GAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTAT
* * * *
43355 TGTATAATAATCCTATAAGAAAATTTATGCAATACACTGTCAGTGTAGTTTAGCAGACTGCACGC
125 TGTATAATAATCCTATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGT
*
43420 ACGAGG
190 ACGGGG
* *
43426 TTTAAGGGTTGACATGTGT-CCTCTTAGGGAATATGTATTAATATTTTATATCAATTAATTATGA
1 TTTAAGGGTTGACATGTGTACC-CTTAGGGAATATGTATTAATA--TTAAAT-ATTTAATTATGA
* * * ** *
43490 AATGGGGTATGCGTCAACTTATTAACCCGCTCATGGAGTTCAAAA-TT-TACAAACAATGTATTG
62 AATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTG
* * * * *
43553 TATAACAATCCTATAAAAAAAATTATACAATACACCGTTAGTAGAGTTTAGCAGACTGCACGTAC
127 TATAATAATCCTATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTAC
**
43618 ATGG
192 GGGG
* * *
43622 TTTAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTATTAATATTAAATATTTAATTAATTATGA
1 TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATA--T--TTAATTATGA
* ** * * * * *
43687 AATGGGGGTATGTATCAACTTCTTAACTAGCTTATGGAGTCCAAAATTTACATTGATAGTGTGTT
62 AAT-GGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATT
*
43752 GTACAATAATCCTTATAA
126 GTATAATAATCC-TATAA
43770 TAAAGCTTAC
Statistics
Matches: 651, Mismatches: 73, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
193 3 0.00
194 45 0.07
196 114 0.18
197 45 0.07
198 56 0.09
199 2 0.00
200 236 0.36
201 150 0.23
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (195 bp):
TTTAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATG
GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATA
ATAATCCTATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTACGGGG
Done.