Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009651.1 Corchorus capsularis cultivar CVL-1 contig09672, 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: 91644
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2970 original size:44 final size:40
Alignment explanation
Indices: 2907--3007 Score: 136
Period size: 37 Copynumber: 2.5 Consensus size: 40
2897 TAACAAGTAG
*
2907 ATTGCTTGAACAAGTAGTTTTTTTTTTTTTTTTAATCGGTGCAT
1 ATTGCTTGAACAAGTAG---TTTTTTTTTTTTT-ATCGGTACAT
2951 ATTGCTTGAACAAGTAG---TTTTTTTTTTATCGGTACAT
1 ATTGCTTGAACAAGTAGTTTTTTTTTTTTTATCGGTACAT
2988 ATTGCTTGAACAAGTAGTTT
1 ATTGCTTGAACAAGTAGTTT
3008 GAATCTTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
37 26 0.49
38 10 0.19
44 17 0.32
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (40 bp):
ATTGCTTGAACAAGTAGTTTTTTTTTTTTTATCGGTACAT
Found at i:2982 original size:37 final size:38
Alignment explanation
Indices: 2930--3007 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 38
2920 GTAGTTTTTT
*
2930 TTTTTTTTTTAATCGGTGCATATTGCTTGAACAAGTAG
1 TTTTTTTTTTAATCGGTACATATTGCTTGAACAAGTAG
2968 TTTTTTTTTT-ATCGGTACATATTGCTTGAACAAGTAG
1 TTTTTTTTTTAATCGGTACATATTGCTTGAACAAGTAG
3005 TTT
1 TTT
3008 GAATCTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 29 0.74
38 10 0.26
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (38 bp):
TTTTTTTTTTAATCGGTACATATTGCTTGAACAAGTAG
Found at i:9488 original size:2 final size:2
Alignment explanation
Indices: 9481--9505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9471 TTTCTAAGCT
9481 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 T
9506 GCCATTCTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16724 original size:29 final size:29
Alignment explanation
Indices: 16659--16739 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
16649 GCTTAATACC
* **
16659 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-TTTTTTGGGA
16690 CAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTTGGGA
*
16719 CAAATTGACCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
16740 AAAAACGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 28 0.61
30 1 0.02
31 17 0.37
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTGGGA
Found at i:17204 original size:127 final size:127
Alignment explanation
Indices: 17026--17281 Score: 485
Period size: 127 Copynumber: 2.0 Consensus size: 127
17016 AAGGTGAGAG
17026 ACGATAATAAACAAAATAAGCAATGTCAGTCTACTGGCATCGAAACAGCCTAAATTTGTGATATG
1 ACGATAATAAACAAAATAAGCAATGTCAGTCTACTGGCATCGAAACAGCCTAAATTTGTGATATG
17091 TCACTCTCTAAGGGATGTCAGTCTTATTCGCCTCATTTTCTTTGTTATTTTTTCTCACCTCC
66 TCACTCTCTAAGGGATGTCAGTCTTATTCGCCTCATTTTCTTTGTTATTTTTTCTCACCTCC
*
17153 ACGATAATAAACAAAATAAGCAATGTCGGTCTACTGGCATCGAAACAGCCTAAATTTGTGATATG
1 ACGATAATAAACAAAATAAGCAATGTCAGTCTACTGGCATCGAAACAGCCTAAATTTGTGATATG
* *
17218 TCACTCTCTAAGGGATGTCGGTCTTATTCGCCTCTTTTTCTTTGTTATTTTTTCTCACCTCC
66 TCACTCTCTAAGGGATGTCAGTCTTATTCGCCTCATTTTCTTTGTTATTTTTTCTCACCTCC
17280 AC
1 AC
17282 AATCAGTAGA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (127 bp):
ACGATAATAAACAAAATAAGCAATGTCAGTCTACTGGCATCGAAACAGCCTAAATTTGTGATATG
TCACTCTCTAAGGGATGTCAGTCTTATTCGCCTCATTTTCTTTGTTATTTTTTCTCACCTCC
Found at i:17696 original size:2 final size:2
Alignment explanation
Indices: 17685--17713 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17675 CTTTTACAGG
17685 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17714 CACACACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40040 original size:2 final size:2
Alignment explanation
Indices: 40033--40078 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
40023 CACATTTCCT
*
40033 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40075 TA TA
1 TA TA
40079 GGATCATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47320 original size:2 final size:2
Alignment explanation
Indices: 47313--47338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47303 TTCTTCCTCC
47313 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
47339 TCACCCTCCA
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:59136 original size:7 final size:7
Alignment explanation
Indices: 59124--59156 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
59114 AACAAGGAAT
59124 TTTTTTC
1 TTTTTTC
59131 TTTTTTTC
1 -TTTTTTC
59139 TTTTTTC
1 TTTTTTC
59146 TTTTTT-
1 TTTTTTC
59152 TTTTT
1 TTTTT
59157 GTAAAACGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.20
7 13 0.52
8 7 0.28
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:59136 original size:8 final size:8
Alignment explanation
Indices: 59123--59156 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
59113 TAACAAGGAA
59123 TTTTTTTC
1 TTTTTTTC
59131 TTTTTTTC
1 TTTTTTTC
59139 -TTTTTTC
1 TTTTTTTC
59146 TTTTTTT-
1 TTTTTTTC
59153 TTTT
1 TTTT
59157 GTAAAACGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTTC
Found at i:59144 original size:15 final size:14
Alignment explanation
Indices: 59123--59156 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
59113 TAACAAGGAA
59123 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
59137 TCTTTTTTCTTTTTT
1 T-TTTTTTCTTTTTT
59152 TTTTT
1 TTTTT
59157 GTAAAACGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:62313 original size:28 final size:27
Alignment explanation
Indices: 62249--62305 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 27
62239 TAATATCCCT
62249 AGAACTCGAATTTGAAACTTTTTTCCAAG
1 AGAA-TCGAATTTGAAACTTTTTT-CAAG
62278 AGAATCGAATTTGAAACTTTATTT-AAG
1 AGAATCGAATTTGAAACTTT-TTTCAAG
62305 A
1 A
62306 ATTATCGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 4 0.15
28 16 0.59
29 7 0.26
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (27 bp):
AGAATCGAATTTGAAACTTTTTTCAAG
Found at i:70270 original size:2 final size:2
Alignment explanation
Indices: 70258--70289 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
70248 TACATTGACA
70258 AT AT A- 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 A
70290 GTGATCAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:72276 original size:2 final size:2
Alignment explanation
Indices: 72269--72304 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
72259 CAAATTAAAT
72269 TA TA TA TA TA TA TA TA TA TA TA TGA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
72305 ACCCAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
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:75107 original size:132 final size:130
Alignment explanation
Indices: 74870--75126 Score: 435
Period size: 132 Copynumber: 2.0 Consensus size: 130
74860 CCCTTGCTTC
*
74870 GATCCTTCATATATATGTCTTATACCTAGTGCAATGTTGTGTGTATGGATTCAGGAACTTTTATT
1 GATCCTTCATATATATGTCTTATACCTAGTGCAATGTTGTGTGTATGGATTCAGGAACTTCTATT
* * *
74935 TACTAGATTCCTTCAAATGTTTTAAATCAATTTTTGTTCATTTTTTGTGAATAATAGACAAAATG
66 TACTAGATTCCTTCAAATGTTTTAAATCAATATTTATTCATGTTTTGTGAATAATAGACAAAATG
*
75000 GATCCTTCATATATATGTCTTATATCTAGTGCAATGTTGCATGTGTATGGATTCAGGAACTTCTA
1 GATCCTTCATATATATGTCTTATACCTAGTGCAATGTTG--TGTGTATGGATTCAGGAACTTCTA
75065 TTTACTAGATTCCTTCAAATG-TTTAAGATCAATATTTATTCATGTTTTGTGAATAATAGACA
64 TTTACTAGATTCCTTCAAATGTTTTAA-ATCAATATTTATTCATGTTTTGTGAATAATAGACA
75127 GACAAAAGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
130 38 0.32
131 5 0.04
132 76 0.64
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (130 bp):
GATCCTTCATATATATGTCTTATACCTAGTGCAATGTTGTGTGTATGGATTCAGGAACTTCTATT
TACTAGATTCCTTCAAATGTTTTAAATCAATATTTATTCATGTTTTGTGAATAATAGACAAAATG
Found at i:76843 original size:36 final size:36
Alignment explanation
Indices: 76790--76899 Score: 175
Period size: 36 Copynumber: 3.1 Consensus size: 36
76780 GAAATCATCT
* *
76790 TCATCATCAAAAACTAATTCTGATGGAACCCAAAGC
1 TCATCATCAAAAGCTAATTCTGAAGGAACCCAAAGC
*
76826 TCATCATCGAAAGCTAATTCTGAAGGAACCCAAAGC
1 TCATCATCAAAAGCTAATTCTGAAGGAACCCAAAGC
* *
76862 TCATCTTCAAAAGCTAATTCTGAAGGAAACCAAAGC
1 TCATCATCAAAAGCTAATTCTGAAGGAACCCAAAGC
76898 TC
1 TC
76900 TGGAGGTTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.22
Consensus pattern (36 bp):
TCATCATCAAAAGCTAATTCTGAAGGAACCCAAAGC
Done.