Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022540.1 Corchorus olitorius cultivar O-4 contig22573, 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: 80689
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:8095 original size:6 final size:6
Alignment explanation
Indices: 8086--8110 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8076 ACATGAGGGG
8086 GGGTCA GGGTCA GGGTCA GGGTCA G
1 GGGTCA GGGTCA GGGTCA GGGTCA G
8111 ATTCCTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGGTCA
Found at i:9522 original size:25 final size:25
Alignment explanation
Indices: 9491--9539 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
9481 TGTTAATTTG
*
9491 TAGAGACCGAGCGAGGGTGCTCAAT
1 TAGAGACCGAGCGAGAGTGCTCAAT
9516 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
9540 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAT
Found at i:10050 original size:14 final size:14
Alignment explanation
Indices: 10031--10059 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10021 TCAATCAATC
10031 CCTCTAATAAAAAG
1 CCTCTAATAAAAAG
10045 CCTCTAATAAAAAG
1 CCTCTAATAAAAAG
10059 C
1 C
10060 AAAGCTAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (14 bp):
CCTCTAATAAAAAG
Found at i:18350 original size:14 final size:15
Alignment explanation
Indices: 18331--18371 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
18321 TATTGAAATA
18331 ATAATAATTATT-TT
1 ATAATAATTATTATT
18345 ATAATAATTATTATT
1 ATAATAATTATTATT
18360 -TCAATAATTATT
1 AT-AATAATTATT
18372 GCTAATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
ATAATAATTATTATT
Found at i:18350 original size:17 final size:17
Alignment explanation
Indices: 18328--18360 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18318 ATTTATTGAA
18328 ATAATAATAATTATTTT
1 ATAATAATAATTATTTT
*
18345 ATAATAATTATTATTT
1 ATAATAATAATTATTT
18361 CAATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAATAATAATTATTTT
Found at i:26972 original size:121 final size:121
Alignment explanation
Indices: 26753--26979 Score: 382
Period size: 121 Copynumber: 1.9 Consensus size: 121
26743 GACCAAGTCC
* * * *
26753 AAAATCGGTAAATCGGCCAGTTCAACCGCGGTTGAACCTGGTCAACGCCGGTATGTTGACTTGAC
1 AAAACCGGTAAATCGGCCAGTTCAACCGCGGTTGAACCGGGTCAACGCCGGTACGTCGACTTGAC
26818 AATTTTATACACATACCGATTCTGGGCACCGGTTCCCGGTTGTCCAAAATCGGTCA
66 AATTTTATACACATACCGATTCTGGGCACCGGTTCCCGGTTGTCCAAAATCGGTCA
* * *
26874 AAAACCGGTAAATCGGCCGGTTCAACCGCGTTTGAATCGGGTCAACGCCGGTACGTCGACTTGAC
1 AAAACCGGTAAATCGGCCAGTTCAACCGCGGTTGAACCGGGTCAACGCCGGTACGTCGACTTGAC
*
26939 AATTTTATACACATACCGGTTCTGGGCACCGGTTCCCGGTT
66 AATTTTATACACATACCGATTCTGGGCACCGGTTCCCGGTT
26980 CAACCGGTTG
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 98 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (121 bp):
AAAACCGGTAAATCGGCCAGTTCAACCGCGGTTGAACCGGGTCAACGCCGGTACGTCGACTTGAC
AATTTTATACACATACCGATTCTGGGCACCGGTTCCCGGTTGTCCAAAATCGGTCA
Found at i:36473 original size:8 final size:8
Alignment explanation
Indices: 36443--36476 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
36433 ACCCTCACTT
36443 AAAAACTAG
1 AAAAA-TAG
*
36452 AAAAAGAG
1 AAAAATAG
36460 AAAAATAG
1 AAAAATAG
36468 AAAAATAG
1 AAAAATAG
36476 A
1 A
36477 TCAAGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (8 bp):
AAAAATAG
Found at i:43588 original size:2 final size:2
Alignment explanation
Indices: 43583--43637 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
43573 AAGGATATCA
* * * * *
43583 AT AT AT TT AT TT AT TT AT AC AT AT AT AT AT AT AT AT AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43624 AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT A
43638 AAAACTGGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:43612 original size:24 final size:26
Alignment explanation
Indices: 43583--43637 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
43573 AAGGATATCA
* *
43583 ATATATTTATTTATTT-ATACA-TAT
1 ATATATATATATATTTAATACATTAT
*
43607 ATATATATATATATTTAATATATTAT
1 ATATATATATATATTTAATACATTAT
43633 ATATA
1 ATATA
43638 AAAACTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 14 0.54
25 4 0.15
26 8 0.31
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATATATATATATTTAATACATTAT
Found at i:51178 original size:206 final size:204
Alignment explanation
Indices: 50815--51232 Score: 694
Period size: 206 Copynumber: 2.0 Consensus size: 204
50805 TTTTAAAAGC
*
50815 TGCGAAAACGCAATTGGGGAGGCTAAGTCCACGAAGCGTTTTCAATGGTTGACTACACGTTGGTG
1 TGCGACAACGCAATTGGGGAGGCTAAGTCCACGAAGCGTTTTCAATGGTTGACTACAC--TGGTG
* *
50880 AAGTTGATGGCCGTAAGCTGACTCATGGCCAAATCATTAGGATCCTGAAGTAGTGAACTGAATTC
64 AAGCTGATGGCCGTAAGCTGACTCATGGCCAAATCATTAGGATCCTCAAGTAGTGAACTGAATTC
* **
50945 AGGCTGAGGTTCGCTTCTTGCTTCCCAAGCGTTTGGATTGTATTTCTTAAGATATCGACTCAATT
129 AGGCTGAGGTTCGCTTCTTACTTCCCAAGCGTTTGGATAATATTTCTTAAGATATCG-C-CAATT
51010 GATTAAATCTTTGG
192 GA-TAAATCTTTGG
*
51024 TGCGACAACGCAATTGGGGAGGCTAAGTCCACGAAGCGTTTTCAATGGTTGACTACAC-GGTTAA
1 TGCGACAACGCAATTGGGGAGGCTAAGTCCACGAAGCGTTTTCAATGGTTGACTACACTGGTGAA
* *
51088 GCTGATGGCCGTAAGCTGACTCATGGCCAAATCATTAGGATCTTCAGGTAGTGAACTGAATTCAG
66 GCTGATGGCCGTAAGCTGACTCATGGCCAAATCATTAGGATCCTCAAGTAGTGAACTGAATTCAG
*
51153 GCTGAGGTTCGCTTCTTACTTCCCAAGCGTTTGGATAATATTTCTTAAGATATCGCCCATTGATA
131 GCTGAGGTTCGCTTCTTACTTCCCAAGCGTTTGGATAATATTTCTTAAGATATCGCCAATTGATA
51218 AATCTTTGG
196 AATCTTTGG
51227 TGCGAC
1 TGCGAC
51233 TTGTTGTCTT
Statistics
Matches: 199, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
203 17 0.09
204 6 0.03
205 1 0.01
206 118 0.59
209 57 0.29
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (204 bp):
TGCGACAACGCAATTGGGGAGGCTAAGTCCACGAAGCGTTTTCAATGGTTGACTACACTGGTGAA
GCTGATGGCCGTAAGCTGACTCATGGCCAAATCATTAGGATCCTCAAGTAGTGAACTGAATTCAG
GCTGAGGTTCGCTTCTTACTTCCCAAGCGTTTGGATAATATTTCTTAAGATATCGCCAATTGATA
AATCTTTGG
Found at i:62170 original size:34 final size:34
Alignment explanation
Indices: 62127--62191 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
62117 TCCTTGAAGA
*
62127 TTTTTTTTTTTT--TGAGATATTGAACAAGTTTG
1 TTTTTTTTTTTTACTAAGATATTGAACAAGTTTG
62159 TTTTTTTTTTTTACTAAGATATTGAACAAGTTT
1 TTTTTTTTTTTTACTAAGATATTGAACAAGTTT
62192 AGTAACATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
34 18 0.60
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (34 bp):
TTTTTTTTTTTTACTAAGATATTGAACAAGTTTG
Found at i:68385 original size:27 final size:27
Alignment explanation
Indices: 68349--68461 Score: 163
Period size: 27 Copynumber: 4.0 Consensus size: 27
68339 GACAACACTA
68349 GATGAAAAGGATGAGCTTCAAGAGAAT
1 GATGAAAAGGATGAGCTTCAAGAGAAT
*
68376 GATGAAAAGGATGAGCTTCAACGAATCATTTAT
1 GATGAAAAGGATGAGCTTCAA-G-A-GA---AT
68409 GATGAAAAGGATGAGCTTCAAGAGAAT
1 GATGAAAAGGATGAGCTTCAAGAGAAT
68436 GATGAAAAGGATGAGCTTCAAGAGAA
1 GATGAAAAGGATGAGCTTCAAGAGAA
68462 AGATTCAGAG
Statistics
Matches: 78, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
27 49 0.63
28 1 0.01
29 1 0.01
30 2 0.03
31 1 0.01
32 1 0.01
33 23 0.29
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (27 bp):
GATGAAAAGGATGAGCTTCAAGAGAAT
Found at i:69226 original size:4 final size:4
Alignment explanation
Indices: 69217--69246 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
69207 TGTCTTTAAT
*
69217 CATA CATA CATA CATA CATA CATG CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
69247 CATACACGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:71950 original size:14 final size:14
Alignment explanation
Indices: 71931--71960 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71921 AAGGGGGAGA
71931 AGTATTATGAATTG
1 AGTATTATGAATTG
*
71945 AGTATTGTGAATTG
1 AGTATTATGAATTG
71959 AG
1 AG
71961 CTTATTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (14 bp):
AGTATTATGAATTG
Found at i:73236 original size:29 final size:29
Alignment explanation
Indices: 73190--73277 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
73180 TTTTTCTGAT
73190 TTTGTTTAAGTGCT-GGTTGTGCACTTGTG
1 TTTGTTTAAGTG-TGGGTTGTGCACTTGTG
* * *
73219 TTTGTTCAAGTGTGGGTTGTACACTTGGG
1 TTTGTTTAAGTGTGGGTTGTGCACTTGTG
* * *
73248 ATTGTTTTGAGTGTGGGTT-TGCACTCGTG
1 TTTG-TTTAAGTGTGGGTTGTGCACTTGTG
73277 T
1 T
73278 CAAAGCTTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
28 1 0.02
29 34 0.72
30 12 0.26
ACGTcount: A:0.11, C:0.10, G:0.33, T:0.45
Consensus pattern (29 bp):
TTTGTTTAAGTGTGGGTTGTGCACTTGTG
Found at i:73909 original size:2 final size:2
Alignment explanation
Indices: 73902--73929 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
73892 CAATCACTTA
73902 AT 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 AT
73930 GAAAATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74128 original size:21 final size:21
Alignment explanation
Indices: 74103--74142 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74093 CAAATCAAGG
74103 AATAAGCAATCAAAGCAAAAC
1 AATAAGCAATCAAAGCAAAAC
*
74124 AATAATCAATCAAAGCAAA
1 AATAAGCAATCAAAGCAAA
74143 GCAAAGCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.12
Consensus pattern (21 bp):
AATAAGCAATCAAAGCAAAAC
Found at i:74303 original size:12 final size:12
Alignment explanation
Indices: 74286--74318 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
74276 TATGAAATCC
74286 TAAAAAGAAAAA
1 TAAAAAGAAAAA
*
74298 TAAAAATAAAAA
1 TAAAAAGAAAAA
74310 T-AAAAGAAA
1 TAAAAAGAAA
74319 GAAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
TAAAAAGAAAAA
Found at i:79724 original size:13 final size:12
Alignment explanation
Indices: 79684--79724 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
79674 AGAAAAGAGC
*
79684 TTTTGAATGTAG
1 TTTTGAATGCAG
79696 TTTTGAATGCAG
1 TTTTGAATGCAG
79708 TTTTGAATGCAAG
1 TTTTGAATGC-AG
79721 TTTT
1 TTTT
79725 TGAGCCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (12 bp):
TTTTGAATGCAG
Done.