Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020816.1 Corchorus olitorius cultivar O-4 contig20849, 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: 113274
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:12494 original size:39 final size:39
Alignment explanation
Indices: 12434--12516 Score: 141
Period size: 39 Copynumber: 2.1 Consensus size: 39
12424 CAGAACAGAA
*
12434 GCGGAGGCGGAAGCAGGAGTGGAAGCGAAGCACAAGGCG
1 GCGGAGGCGGAAGCAGAAGTGGAAGCGAAGCACAAGGCG
12473 GCGGAGGCGGAAGC-GAAAGTGGAAGCGAAGCACAAGGCG
1 GCGGAGGCGGAAGCAG-AAGTGGAAGCGAAGCACAAGGCG
12512 GCGGA
1 GCGGA
12517 AGGGAAGGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
38 1 0.02
39 41 0.98
ACGTcount: A:0.31, C:0.18, G:0.48, T:0.02
Consensus pattern (39 bp):
GCGGAGGCGGAAGCAGAAGTGGAAGCGAAGCACAAGGCG
Found at i:24215 original size:36 final size:32
Alignment explanation
Indices: 24168--24248 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 32
24158 TAGCACAAAT
24168 AAACCATAGAAAT-TTTATTGTTTTGTTGCAAAAAGA
1 AAACCATAGAAATATTT-TT-TTTT-TTG-AAAAA-A
*
24204 AAACCATAGAAAATATTTTTTTTTTTGAAATAA
1 AAACCATAG-AAATATTTTTTTTTTTGAAAAAA
24237 AAACCATAGAAA
1 AAACCATAGAAA
24249 AATAATTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
32 3 0.07
33 10 0.24
34 4 0.10
35 3 0.07
36 13 0.31
37 6 0.14
38 3 0.07
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.35
Consensus pattern (32 bp):
AAACCATAGAAATATTTTTTTTTTTGAAAAAA
Found at i:24245 original size:33 final size:37
Alignment explanation
Indices: 24168--24249 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 37
24158 TAGCACAAAT
24168 AAACCATAG-AAATTTTATTGTTTTGTTGCAAAAAGA
1 AAACCATAGAAAATTTTATTGTTTTGTTGCAAAAAGA
*
24204 AAACCATAGAAAATATTT-TT-TTTT-TTG-AAATA-A
1 AAACCATAGAAAAT-TTTATTGTTTTGTTGCAAAAAGA
24237 AAACCATAGAAAA
1 AAACCATAGAAAA
24250 ATAATTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
33 14 0.33
34 4 0.09
35 3 0.07
36 13 0.30
37 6 0.14
38 3 0.07
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (37 bp):
AAACCATAGAAAATTTTATTGTTTTGTTGCAAAAAGA
Found at i:26878 original size:19 final size:19
Alignment explanation
Indices: 26854--26890 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26844 CTGTTTAGTA
26854 ACTGTACAGATAAGATTAC
1 ACTGTACAGATAAGATTAC
*
26873 ACTGTACAGATTAGATTA
1 ACTGTACAGATAAGATTA
26891 GGTACTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATAAGATTAC
Found at i:30310 original size:7 final size:7
Alignment explanation
Indices: 30298--30331 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
30288 ATTTGAGCTC
30298 GTTGCTA
1 GTTGCTA
30305 GTTGCTA
1 GTTGCTA
30312 GTTGCTA
1 GTTGCTA
*
30319 GTTGCAA
1 GTTGCTA
30326 GTTGCT
1 GTTGCT
30332 GGCTTTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.41
Consensus pattern (7 bp):
GTTGCTA
Found at i:32083 original size:29 final size:28
Alignment explanation
Indices: 32047--32105 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
32037 ATTTGCCATA
*
32047 TAAGATTGATATATA-GAGTTTGAA-ACTT
1 TAAGATTGAGAT-TAGGAGTTT-AATACTT
32075 TAAGTATTGAGATTAGGAGTTTAATACTT
1 TAAG-ATTGAGATTAGGAGTTTAATACTT
32104 TA
1 TA
32106 TCAAAAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.41
Consensus pattern (28 bp):
TAAGATTGAGATTAGGAGTTTAATACTT
Found at i:33612 original size:15 final size:14
Alignment explanation
Indices: 33575--33618 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
33565 CTTTTCCAAA
33575 TAATGGAGAGATTT
1 TAATGGAGAGATTT
**
33589 TTCTGGAGAGATTT
1 TAATGGAGAGATTT
33603 GTAATGGAGAGATTT
1 -TAATGGAGAGATTT
33618 T
1 T
33619 TCTTTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.39
Consensus pattern (14 bp):
TAATGGAGAGATTT
Found at i:38144 original size:15 final size:15
Alignment explanation
Indices: 38124--38162 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
38114 CCTGCTTTCA
*
38124 CTCTGTTTTTGCTTC
1 CTCTGTTTTTGATTC
*
38139 CTCTGTTTTTTATTC
1 CTCTGTTTTTGATTC
38154 CTCTGTTTT
1 CTCTGTTTT
38163 AAGAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.03, C:0.23, G:0.10, T:0.64
Consensus pattern (15 bp):
CTCTGTTTTTGATTC
Found at i:40142 original size:52 final size:50
Alignment explanation
Indices: 40063--40166 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 50
40053 TAATCCTCAT
*
40063 TACAATTTCAAATCATAGATCCTTTTGCTTTTGTGTTATGTATGAACAATTA
1 TACAATTTCAAATCATAGATCCCTTTGC--TTGTGTTATGTATGAACAATTA
40115 TACAATTTCAAATCATAGATCCCTTTGCTTGTGTTATGTATGAACAATTA
1 TACAATTTCAAATCATAGATCCCTTTGCTTGTGTTATGTATGAACAATTA
40165 TA
1 TA
40167 ATGTCAAGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 24 0.47
52 27 0.53
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (50 bp):
TACAATTTCAAATCATAGATCCCTTTGCTTGTGTTATGTATGAACAATTA
Found at i:43235 original size:24 final size:23
Alignment explanation
Indices: 43208--43276 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
43198 AATTATTACA
*
43208 AAAATATAATTTTTAAATTTTTTT
1 AAAATATAATTTTTAAA-TTTTTC
* ***
43232 AAAATTTAAAACTTAAATTTTTC
1 AAAATATAATTTTTAAATTTTTC
* * *
43255 AAAACATATTTTTTAAAATTTT
1 AAAATATAATTTTTAAATTTTT
43277 AATTGCATAT
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAATATAATTTTTAAATTTTTC
Found at i:45755 original size:2 final size:2
Alignment explanation
Indices: 45750--45778 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45740 ATATAATAGG
45750 AT 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 A
45779 GTAGCTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57916 original size:21 final size:19
Alignment explanation
Indices: 57878--57935 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
57868 GCTGCTCTAA
* *
57878 TAATCTAATCTATGCAGTACC
1 TAATCTAATCTGTACAGT--C
*
57899 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTC
*
57918 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
57936 TGCTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTC
Found at i:57923 original size:19 final size:19
Alignment explanation
Indices: 57899--57935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
57889 ATGCAGTACC
57899 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
57918 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
57936 TGCTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:59304 original size:36 final size:36
Alignment explanation
Indices: 59241--59309 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
59231 TTCTCTGGAA
* *
59241 TGTTTGAAATTACTTATGTATTGTGCATCTTTACAT
1 TGTTTGAAATTACTTATATATTATGCATCTTTACAT
* *
59277 TGTTTGAATTTACTTATA-ATATATGCATGTTTA
1 TGTTTGAAATTACTTATATAT-TATGCATCTTTA
59310 ATTACCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 2 0.07
36 26 0.93
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (36 bp):
TGTTTGAAATTACTTATATATTATGCATCTTTACAT
Found at i:73070 original size:10 final size:10
Alignment explanation
Indices: 73055--73091 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
73045 AAAAGGATGG
73055 GAGAGAAAGA
1 GAGAGAAAGA
73065 GAGAGAAGGAGA
1 GAGAGAA--AGA
73077 GAGAGAAAGA
1 GAGAGAAAGA
73087 GAGAG
1 GAGAG
73092 GGAGTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (10 bp):
GAGAGAAAGA
Found at i:73077 original size:12 final size:12
Alignment explanation
Indices: 73062--73091 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
73052 TGGGAGAGAA
*
73062 AGAGAGAGAAGG
1 AGAGAGAGAAAG
73074 AGAGAGAGAAAG
1 AGAGAGAGAAAG
73086 AGAGAG
1 AGAGAG
73092 GGAGTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAAAG
Found at i:77322 original size:58 final size:59
Alignment explanation
Indices: 77258--77378 Score: 208
Period size: 59 Copynumber: 2.1 Consensus size: 59
77248 TTTCCTTTTG
* * *
77258 GGAAAA-TTTGTATCTTTAACTAATTGATTAAATTTGGTCAATTTGGGGCACATGGAAA
1 GGAAAATTTTGCATCTCTAACTAATTGATTAAATTTGGCCAATTTGGGGCACATGGAAA
77316 GGAAAATTTTGCATCTCTAACTAATTGATTAAATTTGGCCAATTTGGGGCACATGGAAA
1 GGAAAATTTTGCATCTCTAACTAATTGATTAAATTTGGCCAATTTGGGGCACATGGAAA
77375 GGAA
1 GGAA
77379 GGGTGGGTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 6 0.10
59 53 0.90
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (59 bp):
GGAAAATTTTGCATCTCTAACTAATTGATTAAATTTGGCCAATTTGGGGCACATGGAAA
Found at i:80583 original size:19 final size:20
Alignment explanation
Indices: 80555--80597 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
80545 TAGAGCATGG
80555 TGAATATC-ATATGACATAA
1 TGAATATCAATATGACATAA
*
80574 TGAATCTCATATATGACATAA
1 TGAATATCA-ATATGACATAA
80595 TGA
1 TGA
80598 GGTAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAATATCAATATGACATAA
Found at i:84652 original size:16 final size:16
Alignment explanation
Indices: 84626--84662 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
84616 GTACCAAGTA
84626 CTTCGTTTTCCTTTTCT
1 CTTC-TTTTCCTTTTCT
84643 CTTCTTTTCCTTTTCT
1 CTTCTTTTCCTTTTCT
84659 -TTCT
1 CTTCT
84663 ATTTTCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 12 0.60
17 4 0.20
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.68
Consensus pattern (16 bp):
CTTCTTTTCCTTTTCT
Found at i:86246 original size:28 final size:29
Alignment explanation
Indices: 86195--86252 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
86185 GTTTTCCTAC
86195 AAAGTCTTAGTGAAAAGGGCTGATCAAGAT
1 AAAGTCTTAG-GAAAAGGGCTGATCAAGAT
*
86225 AAAGTCTTA-GATAAGGGCTGATCAAGAT
1 AAAGTCTTAGGAAAAGGGCTGATCAAGAT
86253 GCATTGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
30 9 0.33
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (29 bp):
AAAGTCTTAGGAAAAGGGCTGATCAAGAT
Found at i:95666 original size:16 final size:16
Alignment explanation
Indices: 95647--95679 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
95637 ACCCTATTCA
95647 ATATTAACCTAAAATC
1 ATATTAACCTAAAATC
95663 ATATTAACCTAAAATC
1 ATATTAACCTAAAATC
95679 A
1 A
95680 AGGGATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATTAACCTAAAATC
Found at i:96321 original size:1 final size:1
Alignment explanation
Indices: 96315--96348 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
96305 ATCTTAAAGC
**
96315 TTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
96349 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:96461 original size:21 final size:22
Alignment explanation
Indices: 96431--96476 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
96421 AGTATGGCTT
* *
96431 AAATTCACTTTTTTAA-AAAAA
1 AAATTAACTTGTTTAAGAAAAA
96452 AAATTAACTTGTTTAAGAAAAA
1 AAATTAACTTGTTTAAGAAAAA
96474 AAA
1 AAA
96477 ACTGTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTAACTTGTTTAAGAAAAA
Found at i:100791 original size:22 final size:22
Alignment explanation
Indices: 100763--100810 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
100753 TTTGAACTTC
100763 CTCATCTTTCTCAATGTTAATA
1 CTCATCTTTCTCAATGTTAATA
*
100785 CTCATCTTTCTCATTGTTAATA
1 CTCATCTTTCTCAATGTTAATA
100807 CTCA
1 CTCA
100811 AACTCAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.46
Consensus pattern (22 bp):
CTCATCTTTCTCAATGTTAATA
Found at i:102233 original size:35 final size:35
Alignment explanation
Indices: 102187--102263 Score: 154
Period size: 35 Copynumber: 2.2 Consensus size: 35
102177 GCTCTTGGGA
102187 TGAACCTTTATAAGGCAGGATTGTGAATAGTGTCC
1 TGAACCTTTATAAGGCAGGATTGTGAATAGTGTCC
102222 TGAACCTTTATAAGGCAGGATTGTGAATAGTGTCC
1 TGAACCTTTATAAGGCAGGATTGTGAATAGTGTCC
102257 TGAACCT
1 TGAACCT
102264 GCAAAACCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (35 bp):
TGAACCTTTATAAGGCAGGATTGTGAATAGTGTCC
Found at i:109682 original size:2 final size:2
Alignment explanation
Indices: 109665--109699 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
109655 TGTTATTATT
*
109665 TA TA TA AA 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 TA TA TA
109700 ATGTTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Done.