Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017329.1 Corchorus olitorius cultivar O-4 contig17362, 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: 19046
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:1073 original size:24 final size:25
Alignment explanation
Indices: 1041--1093 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1031 TTGAATTATT
*
1041 GAGATTTG-AAAGTTTGAAGATTGA
1 GAGAATTGAAAAGTTTGAAGATTGA
* *
1065 GAGAATTGAAAATTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGATTGA
1090 -AGAA
1 GAGAA
1094 AGTAAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGATTGA
Found at i:5325 original size:42 final size:42
Alignment explanation
Indices: 5266--5353 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
5256 GAGATTAACT
5266 TGTTATCAGAAATCAATACAAGAGAGTTGAAAATATTTGTTG
1 TGTTATCAGAAATCAATACAAGAGAGTTGAAAATATTTGTTG
* *
5308 TGTTATCAGAAATCAATACAAGAGAGTTTAAAATTTTTGTTG
1 TGTTATCAGAAATCAATACAAGAGAGTTGAAAATATTTGTTG
5350 TGTT
1 TGTT
5354 TGCCTTCTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (42 bp):
TGTTATCAGAAATCAATACAAGAGAGTTGAAAATATTTGTTG
Found at i:7032 original size:39 final size:39
Alignment explanation
Indices: 6989--7064 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
6979 ATTTATTTGG
*
6989 TATTGCGTTTGGGTTCAAAAGCAGCTTTTTTATCTCCGA
1 TATTGCGTTTGGATTCAAAAGCAGCTTTTTTATCTCCGA
7028 TATTGCGTTTGGATTCAAAAGCAGCTTTTTTATCTCC
1 TATTGCGTTTGGATTCAAAAGCAGCTTTTTTATCTCC
7065 AAACGCAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (39 bp):
TATTGCGTTTGGATTCAAAAGCAGCTTTTTTATCTCCGA
Found at i:7238 original size:13 final size:14
Alignment explanation
Indices: 7217--7268 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 14
7207 ACCTCATCAA
*
7217 TTTTAAAAAGCAC-
1 TTTTCAAAAGCACT
*
7230 TTTTCAAAAGTACT
1 TTTTCAAAAGCACT
*
7244 TTTTCAAAACCAAACT
1 TTTTCAAAAGC--ACT
7260 TTTTCAAAA
1 TTTTCAAAA
7269 CTTAACCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 9 0.28
16 12 0.38
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (14 bp):
TTTTCAAAAGCACT
Found at i:7539 original size:21 final size:23
Alignment explanation
Indices: 7494--7542 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
7484 CATGCACACA
7494 AATATCAATTATTATCTACAAGTT
1 AATATCAATTATTATCTA-AAGTT
7518 AATAT-AATTATTATCT-AAGTT
1 AATATCAATTATTATCTAAAGTT
7539 AATA
1 AATA
7543 ATTAGTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.36
23 11 0.44
24 5 0.20
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (23 bp):
AATATCAATTATTATCTAAAGTT
Found at i:8984 original size:10 final size:10
Alignment explanation
Indices: 8960--9004 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
8950 TTATGCATAT
*
8960 GCTTTAAATG
1 GCTTCAAATG
*
8970 CCTTCAAATG
1 GCTTCAAATG
8980 GCTTCAAATG
1 GCTTCAAATG
8990 GCTTCAAATG
1 GCTTCAAATG
9000 GCTTC
1 GCTTC
9005 TGCCCTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (10 bp):
GCTTCAAATG
Found at i:13457 original size:35 final size:36
Alignment explanation
Indices: 13410--13478 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
13400 TTCAATAACC
*
13410 TTACATCTTTTGTGATTTT-AGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGA-TTATCATATTTCTTA
13446 TTACAT-TTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
13479 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 24 0.77
36 7 0.23
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:14420 original size:202 final size:203
Alignment explanation
Indices: 14031--14427 Score: 742
Period size: 202 Copynumber: 2.0 Consensus size: 203
14021 TTTTTGGTTA
14031 AATGTTATTAATTTTTTAAGTCTAAGATTACAAACAAAGTTGTAGTGAATAAGATACAACACATT
1 AATGTTATTAATTTTTTAAGTCTAAGATTACAAACAAAGTTGTAGTGAATAAGATACAACACATT
*
14096 ATTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTTGAATTATCAAATT
66 ACTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTTGAATTATCAAATT
14161 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTAT
131 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTAT
14226 CAATGGTG
196 CAATGGTG
*
14234 AATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATT
1 AATGTTATTAATTTTTTAAGTCTAAGATTACAAACAAAGTTGTAGTGAATAAGATACAACACATT
* * *
14299 ACTATTATATATAGAACTATACC-AAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATT
66 ACTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTTGAATTATCAAATT
14363 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTAT
131 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTAT
14428 TATTAAGGAA
Statistics
Matches: 189, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
202 104 0.55
203 85 0.45
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (203 bp):
AATGTTATTAATTTTTTAAGTCTAAGATTACAAACAAAGTTGTAGTGAATAAGATACAACACATT
ACTATTATATATAAAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTTGAATTATCAAATT
AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTAT
CAATGGTG
Found at i:14603 original size:42 final size:40
Alignment explanation
Indices: 14535--14618 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 40
14525 AAACCTAAAA
*
14535 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAC
1 ATTTAATTAATGTAAGCATTTCAGTTATTATA-TA-TATTAC
*
14577 ATTTAATTAATGTAAGCATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
14617 AT
1 AT
14619 AGGAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 8 0.20
41 2 0.05
42 30 0.75
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (40 bp):
ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
Found at i:14799 original size:103 final size:103
Alignment explanation
Indices: 14680--14887 Score: 380
Period size: 103 Copynumber: 2.0 Consensus size: 103
14670 TTAATATGAT
*
14680 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTTATTTGATA
1 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
*
14745 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACCAAACTTTTA
*
14783 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATA
1 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
*
14848 AATACATGTTTATCCTTTAAATGAATACCAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACCAAACTTTTA
14886 AA
1 AA
14888 ATTAAAAAGG
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (103 bp):
AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
AATACATGTTTACCCTTTAAATGAATACCAAACTTTTA
Found at i:14985 original size:6 final size:6
Alignment explanation
Indices: 14950--15018 Score: 106
Period size: 6 Copynumber: 11.8 Consensus size: 6
14940 TATATAGTAA
* *
14950 ATATAG ATATAA ATATAA ATATAG ATATAG ATATAG --ATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
14996 ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATA
15019 TATTAAAGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.07
6 55 0.93
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:14991 original size:10 final size:10
Alignment explanation
Indices: 14976--15010 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
14966 AAATATAGAT
14976 ATAGATATAG
1 ATAGATATAG
14986 ATAGATATAG
1 ATAGATATAG
14996 ATATAGATATAG
1 --ATAGATATAG
15008 ATA
1 ATA
15011 TAGATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (10 bp):
ATAGATATAG
Found at i:14996 original size:22 final size:22
Alignment explanation
Indices: 14947--15010 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
14937 ACTTATATAG
14947 TAAATATAGATATA-A-AT--A
1 TAAATATAGATATAGATATAGA
14965 TAAATATAGATATAGATATAGA
1 TAAATATAGATATAGATATAGA
*
14987 TAGATATAGATATAGATATAGA
1 TAAATATAGATATAGATATAGA
15009 TA
1 TA
15011 TAGATATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 14 0.34
19 1 0.02
20 2 0.05
22 24 0.59
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (22 bp):
TAAATATAGATATAGATATAGA
Found at i:14999 original size:28 final size:28
Alignment explanation
Indices: 14962--15021 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
14952 ATAGATATAA
14962 ATATAAATATAGATATAGATATAGATAG
1 ATATAAATATAGATATAGATATAGATAG
* *
14990 ATATAGATATAGATATAGATATAGATAT
1 ATATAAATATAGATATAGATATAGATAG
15018 ATAT
1 ATAT
15022 TAAAGAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (28 bp):
ATATAAATATAGATATAGATATAGATAG
Found at i:15215 original size:13 final size:13
Alignment explanation
Indices: 15197--15224 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15187 CTCTTTGGGC
15197 TTTGTTTTCCACT
1 TTTGTTTTCCACT
15210 TTTGTTTTCCACT
1 TTTGTTTTCCACT
15223 TT
1 TT
15225 GCTTTCGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTGTTTTCCACT
Found at i:15225 original size:12 final size:12
Alignment explanation
Indices: 15196--15230 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
15186 CCTCTTTGGG
15196 CTTTGTTTTCCA
1 CTTTGTTTTCCA
15208 CTTTTGTTTTCCA
1 C-TTTGTTTTCCA
*
15221 CTTTGCTTTC
1 CTTTGTTTTC
15231 GACCTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.06, C:0.26, G:0.09, T:0.60
Consensus pattern (12 bp):
CTTTGTTTTCCA
Found at i:15354 original size:22 final size:21
Alignment explanation
Indices: 15302--15382 Score: 85
Period size: 22 Copynumber: 3.9 Consensus size: 21
15292 TGAATATTTT
*
15302 TATGAAATTTTGATAAATACCC
1 TATGAAATTTTGATAAATA-TC
*
15324 TA--AAATTTTGATAACTATC
1 TATGAAATTTTGATAAATATC
*
15343 ATATGAAATTTTGATAATTATC
1 -TATGAAATTTTGATAAATATC
* *
15365 TATAAAATTGTGATAAAT
1 TATGAAATTTTGATAAAT
15383 TCCATAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.02
20 16 0.32
21 15 0.30
22 18 0.36
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAAATATC
Found at i:15391 original size:20 final size:21
Alignment explanation
Indices: 15306--15391 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 21
15296 TATTTTTATG
*
15306 AAATTTTGATAAATA-CCCTA
1 AAATTTTGATAAATATCCATA
*
15326 AAATTTTGATAACTAT-CATA
1 AAATTTTGATAAATATCCATA
* *
15346 TGAAATTTTGATAATTATCTATA
1 --AAATTTTGATAAATATCCATA
*
15369 AAATTGTGATAAAT-TCCATA
1 AAATTTTGATAAATATCCATA
15389 AAA
1 AAA
15392 AAACTTAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
20 25 0.45
21 12 0.22
22 15 0.27
23 3 0.05
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAAATATCCATA
Done.