Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013484.1 Corchorus olitorius cultivar O-4 contig13517, 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: 32720
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1839 original size:29 final size:29
Alignment explanation
Indices: 1797--1881 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
1787 TACAAGTTTA
1797 CAACACCACAATTACAAGTTTTCAACAAT
1 CAACACCACAATTACAAGTTTTCAACAAT
1826 CAACACCACAATTACAAGTTTTCAACAAT
1 CAACACCACAATTACAAGTTTTCAACAAT
*
1855 CAACACCACAATTACAAGCTTTCAACA
1 CAACACCACAATTACAAGTTTTCAACA
1882 CCGTGCAAGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.45, C:0.29, G:0.04, T:0.22
Consensus pattern (29 bp):
CAACACCACAATTACAAGTTTTCAACAAT
Found at i:1969 original size:29 final size:29
Alignment explanation
Indices: 1937--2000 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1927 TATCAAATCC
1937 ATCATCCAAATAAAATTCATGAAATAATT
1 ATCATCCAAATAAAATTCATGAAATAATT
*
1966 ATCATCCAAATGAAATTCATGAAATAATT
1 ATCATCCAAATAAAATTCATGAAATAATT
1995 ATCATC
1 ATCATC
2001 TTGCACTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (29 bp):
ATCATCCAAATAAAATTCATGAAATAATT
Found at i:1999 original size:14 final size:14
Alignment explanation
Indices: 1953--1999 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1943 CAAATAAAAT
1953 TCATGAAATAATTA
1 TCATGAAATAATTA
* *
1967 TCATCCAAATGAAAT-
1 TCAT-GAAAT-AATTA
1982 TCATGAAATAATTA
1 TCATGAAATAATTA
1996 TCAT
1 TCAT
2000 CTTGCACTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.12
14 12 0.46
15 8 0.31
16 3 0.12
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (14 bp):
TCATGAAATAATTA
Found at i:3020 original size:50 final size:49
Alignment explanation
Indices: 2941--3035 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 49
2931 TGATAATTCA
* *
2941 TAAAAACAATAAATATAATAAATCGCATATGAATTTGTAATCATAAAAAT
1 TAAAAAAAATAAATATAATAAATCACATATGAATTTGTAAT-ATAAAAAT
* *
2991 TAAAAAAAATTAATATAATAAATCACATATTAATTTGTAATATAA
1 TAAAAAAAATAAATATAATAAATCACATATGAATTTGTAATATAA
3036 CATAAAAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 4 0.10
50 37 0.90
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (49 bp):
TAAAAAAAATAAATATAATAAATCACATATGAATTTGTAATATAAAAAT
Found at i:5685 original size:48 final size:48
Alignment explanation
Indices: 5633--5730 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
5623 ACATTAATTT
5633 AATACCAAAATATTATAAGATTAGAGCAAAACATAACACTCATGAATC
1 AATACCAAAATATTATAAGATTAGAGCAAAACATAACACTCATGAATC
* *
5681 AATACCAAAATATTATGAGATTAGAGCAAATCATAACACTCATGAATC
1 AATACCAAAATATTATAAGATTAGAGCAAAACATAACACTCATGAATC
5729 AA
1 AA
5731 AATAGTTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (48 bp):
AATACCAAAATATTATAAGATTAGAGCAAAACATAACACTCATGAATC
Found at i:6364 original size:134 final size:135
Alignment explanation
Indices: 6115--6378 Score: 512
Period size: 134 Copynumber: 2.0 Consensus size: 135
6105 CTACTAATAT
*
6115 ATAATTATAAGTTTAACAATTATAAGGCATCTCAATTTCATTGTCAGTCTAGATGAAGGTGATTT
1 ATAATAATAAGTTTAACAATTATAAGGCATCTCAATTTCATTGTCAGTCTAGATGAAGGTGATTT
6180 CTTGAAACTGTACGTAGGGGCATACAAAATGCTCAAGTTCGTCGAAGTTGTAAGGATATGATTAG
66 CTTGAAACTGTACGTAGGGGCATACAAAATGCTCAAGTTCGTCGAAGTTGTAAGGATATGATTAG
6245 TAATG
131 TAATG
6250 ATAATAAT-AGTTTAACAATTATAAGGCATCTCAATTTCATTGTCAGTCTAGATGAAGGTGATTT
1 ATAATAATAAGTTTAACAATTATAAGGCATCTCAATTTCATTGTCAGTCTAGATGAAGGTGATTT
6314 CTTGAAACTGTACGTAGGGGCATACAAAATGCTCAAGTTCGTCGAAGTTGTAAGGATATGATTAG
66 CTTGAAACTGTACGTAGGGGCATACAAAATGCTCAAGTTCGTCGAAGTTGTAAGGATATGATTAG
6379 AAGTCATGAT
Statistics
Matches: 128, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
134 121 0.95
135 7 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (135 bp):
ATAATAATAAGTTTAACAATTATAAGGCATCTCAATTTCATTGTCAGTCTAGATGAAGGTGATTT
CTTGAAACTGTACGTAGGGGCATACAAAATGCTCAAGTTCGTCGAAGTTGTAAGGATATGATTAG
TAATG
Found at i:7397 original size:20 final size:20
Alignment explanation
Indices: 7372--7410 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7362 CATATAAAAT
*
7372 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
7392 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
7411 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:11782 original size:11 final size:11
Alignment explanation
Indices: 11762--11796 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
11752 TTGACAGCGC
11762 AACAAAAACAA
1 AACAAAAACAA
*
11773 AACGAAAACAA
1 AACAAAAACAA
11784 AACAAAAACAA
1 AACAAAAACAA
11795 AA
1 AA
11797 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:15231 original size:21 final size:21
Alignment explanation
Indices: 15207--15250 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
15197 ATGATCCATC
15207 TAATAATTTCTCCTCATTTAG
1 TAATAATTTCTCCTCATTTAG
15228 TAATAATTTCTCCTCATTTAG
1 TAATAATTTCTCCTCATTTAG
15249 TA
1 TA
15251 TAGTTGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (21 bp):
TAATAATTTCTCCTCATTTAG
Found at i:15431 original size:20 final size:23
Alignment explanation
Indices: 15406--15448 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
15396 AAGAATATTG
15406 TTGTTG-AAG-AAAAT-AAAAAT
1 TTGTTGAAAGTAAAATGAAAAAT
15426 TTGTTGAAAGTAAAATGAAAAAT
1 TTGTTGAAAGTAAAATGAAAAAT
15449 AAAAATTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 3 0.15
22 5 0.25
23 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (23 bp):
TTGTTGAAAGTAAAATGAAAAAT
Found at i:19303 original size:26 final size:26
Alignment explanation
Indices: 19267--19319 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
19257 TGGGTTCACC
19267 ATGTTGGAAAATGGTACTAATTCCTA
1 ATGTTGGAAAATGGTACTAATTCCTA
*
19293 ATGTTGGAAAATGGTAGTAATTCCTA
1 ATGTTGGAAAATGGTACTAATTCCTA
19319 A
1 A
19320 GTTTTTACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (26 bp):
ATGTTGGAAAATGGTACTAATTCCTA
Found at i:20522 original size:20 final size:20
Alignment explanation
Indices: 20478--20516 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20468 ATTCCGTTGT
*
20478 TTAATATCTAACGCAACGAC
1 TTAAGATCTAACGCAACGAC
20498 TTAAGATCTAACGCAACGA
1 TTAAGATCTAACGCAACGA
20517 TCTAAGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (20 bp):
TTAAGATCTAACGCAACGAC
Found at i:21021 original size:202 final size:201
Alignment explanation
Indices: 20658--21229 Score: 903
Period size: 200 Copynumber: 2.8 Consensus size: 201
20648 TGTGAAAATT
*
20658 TTTTTGCAACCACTTTAATTGGTTACGGATAACTTTTAAAAATGATTAAATATCGTTTCCAAAAC
1 TTTTTGCAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATATCGTTTCCAAAAC
* * * *
20723 ACTTACGTAACGACCTCTAGATAGTTGCCAAAATAATTTAAAAACGATTAAATGTCATTACGAAA
66 ACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAA
* * * *
20788 ATCCTTACACAACGACGTTGTTTTAGTTGTGAAATCTTTTACGTAGCAACATTCGATTGGTTGTG
131 ACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTCGATTGGTTGCG
20853 TAATAA
196 TAATAA
* * *
20859 TTTTTGTAACCACTTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAAAATTGTTTCCAAAA
1 TTTTTGCAACCAC-TTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATATCGTTTCCAAAA
* * * *
20924 CACTTACATAACAATCTTTAGGTAGTTGTCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAA
65 CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAA
* *
20989 AACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATC-TTTACGTATCAACATTTGATTGGTTGC
130 AACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTCGATTGGTTGC
21053 GTAATAA
195 GTAATAA
* * *
21060 TTTTTGCAACCACTTTAATTGGTTATGAATAACTTTTAGAAATGATTAAATGTCGTTTCCAAAAC
1 TTTTTGCAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATATCGTTTCCAAAAC
* * *
21125 ACTTATATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTATATATCGTTGCGAAA
66 ACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAA
*
21190 ACCCTTACGCAACGATGTTGTTTTGGTTGTGAAATCTTTT
131 ACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTT
21230 GAATGGCTTT
Statistics
Matches: 337, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
200 140 0.42
201 58 0.17
202 139 0.41
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (201 bp):
TTTTTGCAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATATCGTTTCCAAAAC
ACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAA
ACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTCGATTGGTTGCG
TAATAA
Found at i:28625 original size:2 final size:2
Alignment explanation
Indices: 28618--28648 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28608 TCCATAAAAG
28618 AT 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 AT A
28649 AGGAGAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29024 original size:2 final size:2
Alignment explanation
Indices: 29017--29046 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29007 TCTTGAGAAG
*
29017 CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29047 GTCCCCTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:29992 original size:18 final size:18
Alignment explanation
Indices: 29965--30026 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
29955 ATTCTTATGT
*
29965 AATACATATAATAACTAA
1 AATACGTATAATAACTAA
* *
29983 AATACGTATATTAATTAA
1 AATACGTATAATAACTAA
* *
30001 ATGTAATGCTATAATAACTAA
1 A-AT-ACG-TATAATAACTAA
30022 AATAC
1 AATAC
30027 TTACATTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
18 16 0.50
19 2 0.06
20 3 0.09
21 11 0.34
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (18 bp):
AATACGTATAATAACTAA
Found at i:30016 original size:39 final size:40
Alignment explanation
Indices: 29961--30041 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
29951 TTTAATTCTT
*
29961 ATGTAATACATATAATAACTAAAATACGTATATTAATTAA
1 ATGTAATACATATAATAACTAAAATACGTACATTAATTAA
* *
30001 ATGTAATGC-TATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATACATATAATAACTAAAATACGTACATTAATTAA
30040 AT
1 AT
30042 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (40 bp):
ATGTAATACATATAATAACTAAAATACGTACATTAATTAA
Found at i:30531 original size:205 final size:205
Alignment explanation
Indices: 30155--30566 Score: 738
Period size: 205 Copynumber: 2.0 Consensus size: 205
30145 CTTAATAATG
*
30155 AATAAATCGGATCTTAATATCTTTTATAATTTTGAAGTTTTGTTTGACATTGATCTAATTTAATT
1 AATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
*
30220 TAATAAATCAACCACTAATATTCAACTAATTTTTTTGGTATAGTTCTATATTATATATAATAGTA
66 TAATAAATCAACCACTAATATTCAACTAATTTTTTTGGTATAGTTCTATATTATATATAATAATA
*
30285 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTC
30350 ACCATTGATA
196 ACCATTGATA
30360 AATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAAT
1 AATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAAT
* * *
30425 TTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATA-TATA-ATAATAA
65 TTAATAAATCAACCACTAATATTCAACTA-ATTTTTTTGGTATAGTTCTATATTATATATAATAA
30488 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
129 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACAT
30553 TCACCATTGATA
194 TCACCATTGATA
30565 AA
1 AA
30567 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
205 97 0.49
206 82 0.41
207 20 0.10
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (205 bp):
AATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
TAATAAATCAACCACTAATATTCAACTAATTTTTTTGGTATAGTTCTATATTATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTC
ACCATTGATA
Found at i:32389 original size:36 final size:36
Alignment explanation
Indices: 32342--32411 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
32332 GAGATTTTGG
*
32342 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
*
32378 AGAAATATGATAACCAAAATTACAAAAGATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
32412 GGTTGTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Done.