Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020841.1 Corchorus olitorius cultivar O-4 contig20874, 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: 97036
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2149 original size:21 final size:21
Alignment explanation
Indices: 2103--2154 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
2093 ATTTTAATCC
*
2103 GTGTTTGT-GGCTCGATTGGTT
1 GTGTTTGTGGGCTCGAAT-GTT
2124 GTGTTTGTGGGCTCGAAT-TT
1 GTGTTTGTGGGCTCGAATGTT
2144 GATGTTGTGTG
1 G-TGTT-TGTG
2155 ATCAACTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 12 0.44
22 12 0.44
ACGTcount: A:0.08, C:0.08, G:0.38, T:0.46
Consensus pattern (21 bp):
GTGTTTGTGGGCTCGAATGTT
Found at i:4279 original size:11 final size:11
Alignment explanation
Indices: 4259--4294 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
4249 TTGACAGCGC
4259 AACAAAAACAA
1 AACAAAAACAA
*
4270 AACGAAAACAA
1 AACAAAAACAA
4281 AACAAAAACTAA
1 AACAAAAAC-AA
4293 AA
1 AA
4295 ACAGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.78, C:0.17, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:8570 original size:10 final size:10
Alignment explanation
Indices: 8555--8593 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
8545 TCTACCTGAG
8555 AAGCTCTATT
1 AAGCTCTATT
*
8565 AAGCTCTACT
1 AAGCTCTATT
8575 AAGCTCTATT
1 AAGCTCTATT
*
8585 ATGCTCTAT
1 AAGCTCTAT
8594 CACACCCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (10 bp):
AAGCTCTATT
Found at i:8580 original size:20 final size:20
Alignment explanation
Indices: 8555--8592 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8545 TCTACCTGAG
8555 AAGCTCTATTAAGCTCTACT
1 AAGCTCTATTAAGCTCTACT
*
8575 AAGCTCTATTATGCTCTA
1 AAGCTCTATTAAGCTCTA
8593 TCACACCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
AAGCTCTATTAAGCTCTACT
Found at i:9216 original size:18 final size:18
Alignment explanation
Indices: 9193--9238 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
9183 ATGGCTGCTT
9193 GAGAGAGAAAGAAGGGAA
1 GAGAGAGAAAGAAGGGAA
9211 GAGAGAGAAAGAAGGGAA
1 GAGAGAGAAAGAAGGGAA
9229 GAGAGAGAAA
1 GAGAGAGAAA
9239 CGACCGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (18 bp):
GAGAGAGAAAGAAGGGAA
Found at i:16599 original size:2 final size:2
Alignment explanation
Indices: 16592--16622 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16582 ATTAGTAGAT
16592 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
16623 GGTAGTACCC
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:27006 original size:51 final size:51
Alignment explanation
Indices: 26872--26993 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
26862 TGGCGGAGGA
* * *
26872 GGAGGAGGAGGCGGCGGTGGTGCAACTTGATTCACTGCTGCTACTGGTGCT
1 GGAGGTGGAGGAGGCGGTGGTGCAACTTGCTTCACTGCTGCTACTGGTGCT
* *
26923 GGTGGTGGAGGAGGCGGGGGTGCAACTTGCTTCACTGCTGCTACTGGTGCT
1 GGAGGTGGAGGAGGCGGTGGTGCAACTTGCTTCACTGCTGCTACTGGTGCT
*
26974 GGAGGTGGCGGAGGCGGTGG
1 GGAGGTGGAGGAGGCGGTGG
26994 AGGAATTTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.13, C:0.18, G:0.47, T:0.22
Consensus pattern (51 bp):
GGAGGTGGAGGAGGCGGTGGTGCAACTTGCTTCACTGCTGCTACTGGTGCT
Found at i:36001 original size:36 final size:36
Alignment explanation
Indices: 35954--36037 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
35944 TTTTTTGGAA
*
35954 TCCTCTGTTTTTACTCAAACTTATAGGTATGCAATC
1 TCCTCTGTTTTTACTCAAACTTATAGGTATGAAATC
*
35990 TCCTCTGTTTTTACTCAAACTTATAGGTGTGAAATC
1 TCCTCTGTTTTTACTCAAACTTATAGGTATGAAATC
36026 TCCTCTGTTTTT
1 TCCTCTGTTTTT
36038 TCCTCTGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (36 bp):
TCCTCTGTTTTTACTCAAACTTATAGGTATGAAATC
Found at i:36042 original size:48 final size:48
Alignment explanation
Indices: 35990--36100 Score: 195
Period size: 48 Copynumber: 2.3 Consensus size: 48
35980 GTATGCAATC
*
35990 TCCTCTGTTTTTACTCAAACTTATAGGTGTGAAATCTCCTCTGTTTTT
1 TCCTCTGTTTTTACTCAAACTTATAGGTATGAAATCTCCTCTGTTTTT
*
36038 TCCTCTGTTTTTACTCAAACTTATAGGTATGCAATCTCCTCTGTTTTT
1 TCCTCTGTTTTTACTCAAACTTATAGGTATGAAATCTCCTCTGTTTTT
*
36086 TCCTCTGATTTTACT
1 TCCTCTGTTTTTACT
36101 GTTTTTAGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.49
Consensus pattern (48 bp):
TCCTCTGTTTTTACTCAAACTTATAGGTATGAAATCTCCTCTGTTTTT
Found at i:41110 original size:29 final size:29
Alignment explanation
Indices: 41068--41123 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
41058 TCAGTTTAAA
41068 TAAGTCTTAAGTTCGAGATCTTGCATACT
1 TAAGTCTTAAGTTCGAGATCTTGCATACT
41097 TAAGTCTTAAGTTCGAGATCTTGCATA
1 TAAGTCTTAAGTTCGAGATCTTGCATA
41124 TGCAGCAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (29 bp):
TAAGTCTTAAGTTCGAGATCTTGCATACT
Found at i:55595 original size:2 final size:2
Alignment explanation
Indices: 55588--55618 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55578 ATGATGTAAG
55588 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
55619 GGTCAACTCA
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:74720 original size:2 final size:2
Alignment explanation
Indices: 74713--74756 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
74703 ATTATTAACC
74713 TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
74755 TA
1 TA
74757 AGGCCACCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76616 original size:3 final size:3
Alignment explanation
Indices: 76608--76641 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
76598 TGAGACCTTC
76608 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
76642 GATGGACCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:77315 original size:2 final size:2
Alignment explanation
Indices: 77308--77348 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
77298 CTCAGGCAAG
77308 TA TA 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 TA TA T
77349 TTCCCACGAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84171 original size:53 final size:53
Alignment explanation
Indices: 84091--84224 Score: 250
Period size: 53 Copynumber: 2.5 Consensus size: 53
84081 AACATTAATT
*
84091 AATTGCATAAAGACATGATTTTTACTATAAGAAAACACTAACCCATGCTGAAG
1 AATTGCATAAAGACATCATTTTTACTATAAGAAAACACTAACCCATGCTGAAG
*
84144 AATTGCATAAAGACATCATCTTTACTATAAGAAAACACTAACCCATGCTGAAG
1 AATTGCATAAAGACATCATTTTTACTATAAGAAAACACTAACCCATGCTGAAG
84197 AATTGCATAAAGACATCATTTTTACTAT
1 AATTGCATAAAGACATCATTTTTACTAT
84225 GAATTATAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 78 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (53 bp):
AATTGCATAAAGACATCATTTTTACTATAAGAAAACACTAACCCATGCTGAAG
Found at i:90807 original size:21 final size:21
Alignment explanation
Indices: 90783--90822 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
90773 CAATTAAACT
*
90783 ATTAAACTTCTGAAATTTTCA
1 ATTAAACTACTGAAATTTTCA
*
90804 ATTAAACTACTGAACTTTT
1 ATTAAACTACTGAAATTTT
90823 AAAAATGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTAAACTACTGAAATTTTCA
Found at i:91734 original size:7 final size:7
Alignment explanation
Indices: 91722--91755 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
91712 AAGAAATCGA
91722 TTGAGAG
1 TTGAGAG
91729 TTGAGAG
1 TTGAGAG
91736 TTGAGAG
1 TTGAGAG
91743 TTGAGAG
1 TTGAGAG
91750 TTGAGA
1 TTGAGA
91756 CCCTTCTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (7 bp):
TTGAGAG
Found at i:92743 original size:24 final size:23
Alignment explanation
Indices: 92692--92749 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
92682 CGGCAATTTT
* *
92692 TTTTTACTTCTTTTTTATGTTCA
1 TTTTTACTTTTTTTTTATATTCA
92715 TTTTTACTTTTTTTTTAGTTATTCA
1 TTTTTACTTTTTTTTTA--TATTCA
92740 -TTTTACTTTT
1 TTTTTACTTTT
92750 GTTGCTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 16 0.52
24 10 0.32
25 5 0.16
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.72
Consensus pattern (23 bp):
TTTTTACTTTTTTTTTATATTCA
Found at i:94232 original size:7 final size:7
Alignment explanation
Indices: 94220--94245 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
94210 CAAACTACTC
94220 TCTCAGT
1 TCTCAGT
94227 TCTCAGT
1 TCTCAGT
94234 TCTCAGT
1 TCTCAGT
94241 TCTCA
1 TCTCA
94246 CTCACCTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.12, T:0.42
Consensus pattern (7 bp):
TCTCAGT
Done.