Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016995.1 Corchorus olitorius cultivar O-4 contig17028, 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: 95640
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:572 original size:13 final size:12
Alignment explanation
Indices: 551--585 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
541 AATAAAGTAA
551 TAATACTATTAT
1 TAATACTATTAT
*
563 TGATTACTATTAT
1 T-AATACTATTAT
576 TAATACTATT
1 TAATACTATT
586 TCAATGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Found at i:4849 original size:29 final size:30
Alignment explanation
Indices: 4799--4863 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
4789 TGGTAAAACG
* *
4799 TCCAAAATTTAGAATTCAAGGGGCAAAATA
1 TCCAAAATTGAGAATTCAAGGGACAAAATA
* *
4829 TCCAAAATTGA-AATTGAAGGGACAAAATG
1 TCCAAAATTGAGAATTCAAGGGACAAAATA
4858 TCCAAA
1 TCCAAA
4864 TGCTACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.22
Consensus pattern (30 bp):
TCCAAAATTGAGAATTCAAGGGACAAAATA
Found at i:8181 original size:30 final size:30
Alignment explanation
Indices: 8145--8204 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
8135 AGAAGAATGC
* *
8145 TTCCTTATTATTACTATATTGTAGCAGCAA
1 TTCCTTACTACTACTATATTGTAGCAGCAA
* *
8175 TTCCTTACTACTACTTTGTTGTAGCAGCAA
1 TTCCTTACTACTACTATATTGTAGCAGCAA
8205 CCAACCATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.42
Consensus pattern (30 bp):
TTCCTTACTACTACTATATTGTAGCAGCAA
Found at i:17606 original size:60 final size:60
Alignment explanation
Indices: 17542--17655 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
17532 ATAAGGGACT
* *
17542 GATCTTTTAATTTGGTCAAATAAGGGCGT-AACGTTATAAAAAATGCTCAAATAATGACCC
1 GATCTTTTAATTTGGCCAAATAAGGAC-TCAACGTTATAAAAAATGCTCAAATAATGACCC
* **
17602 GATCTTTTAATTTGGCCAAATAAGGACTCAATGTTATCGAAAATGCTCAAATAA
1 GATCTTTTAATTTGGCCAAATAAGGACTCAACGTTATAAAAAATGCTCAAATAA
17656 GGGCCTAGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (60 bp):
GATCTTTTAATTTGGCCAAATAAGGACTCAACGTTATAAAAAATGCTCAAATAATGACCC
Found at i:17895 original size:27 final size:27
Alignment explanation
Indices: 17824--17887 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
17814 TTCATCAAGT
*
17824 ACTTTAACTGATGGCCAAATAAATTCA
1 ACTTTAAATGATGGCCAAATAAATTCA
17851 ACTTTAAATGATGGCCAAATAAATTCA
1 ACTTTAAATGATGGCCAAATAAATTCA
17878 ACTTTAAATG
1 ACTTTAAATG
17888 TTTTCCAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (27 bp):
ACTTTAAATGATGGCCAAATAAATTCA
Found at i:26219 original size:13 final size:13
Alignment explanation
Indices: 26191--26224 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
26181 ACTGTAAACG
26191 TTTAAAAATATCA
1 TTTAAAAATATCA
26204 TTTAAGAAATAT-A
1 TTTAA-AAATATCA
26217 TTTAAAAA
1 TTTAAAAA
26225 ATTATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 11 0.55
14 6 0.30
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (13 bp):
TTTAAAAATATCA
Found at i:26327 original size:84 final size:83
Alignment explanation
Indices: 26235--26391 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 83
26225 ATTATAATAT
* *
26235 ATATATCTAAG-TTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAATGAGATC
1 ATATATCTAAGTTTATGTAATTAAAATAGT-AAAATGGTAAAAATAAAATAATTATAAAGA-ATC
26299 AGATTTAATTAAAAATTCTA
64 AGATTTAATTAAAAATTCTA
* * * * *
26319 ATATATCTAAGTTTTTTTAATTAAAATTGTAAAATTGTAAAAATAAAATAATTATAAAGAATTAG
1 ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAATTATAAAGAATCAG
26384 ATTTAATT
66 ATTTAATT
26392 GAATAAAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 12 0.18
84 38 0.58
85 15 0.23
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (83 bp):
ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAATTATAAAGAATCAG
ATTTAATTAAAAATTCTA
Found at i:35473 original size:14 final size:14
Alignment explanation
Indices: 35454--35480 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35444 GAAATATTGA
35454 TTTTTTTTTAGAAC
1 TTTTTTTTTAGAAC
35468 TTTTTTTTTAGAA
1 TTTTTTTTTAGAA
35481 GGTAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTTTTTAGAAC
Found at i:37627 original size:22 final size:23
Alignment explanation
Indices: 37577--37628 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
37567 ATTGCATACA
*
37577 TCTTTACATGACTTTATCATACT
1 TCTTTACATGACTTTATCAGACT
* *
37600 TTTTTACATGACTTTCTC-GACT
1 TCTTTACATGACTTTATCAGACT
37622 TCTTTAC
1 TCTTTAC
37629 CACAAGATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.50
Consensus pattern (23 bp):
TCTTTACATGACTTTATCAGACT
Found at i:37917 original size:12 final size:12
Alignment explanation
Indices: 37900--37925 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37890 TCATAGTTTC
37900 ATTATAAAAGTA
1 ATTATAAAAGTA
37912 ATTATAAAAGTA
1 ATTATAAAAGTA
37924 AT
1 AT
37926 AGTACAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
ATTATAAAAGTA
Found at i:53538 original size:2 final size:2
Alignment explanation
Indices: 53527--53558 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
53517 AGATATTTAT
53527 TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53559 CTAATACGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60496 original size:15 final size:16
Alignment explanation
Indices: 60476--60505 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
60466 TGCAAGTTTA
60476 AAAAACTT-GTTGACG
1 AAAAACTTGGTTGACG
60491 AAAAACTTGGTTGAC
1 AAAAACTTGGTTGAC
60506 ATAATATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (16 bp):
AAAAACTTGGTTGACG
Found at i:60992 original size:9 final size:9
Alignment explanation
Indices: 60980--61004 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60970 CCATCATAAC
60980 CATAATCCT
1 CATAATCCT
60989 CATAATCCT
1 CATAATCCT
60998 CATAATC
1 CATAATC
61005 ATAGACTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (9 bp):
CATAATCCT
Found at i:68361 original size:1 final size:1
Alignment explanation
Indices: 68355--68405 Score: 75
Period size: 1 Copynumber: 51.0 Consensus size: 1
68345 AAGTTTAGAC
* * *
68355 AAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
68406 CAAACCATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:68381 original size:19 final size:19
Alignment explanation
Indices: 68357--68405 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
68347 GTTTAGACAA
68357 AAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAC
*
68376 AAAAAAAACAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAC
68395 AAAAAAAAAAA
1 AAAAAAAAAAA
68406 CAAACCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAC
Found at i:71249 original size:34 final size:38
Alignment explanation
Indices: 71179--71255 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
71169 GACATCCACA
*
71179 ACATACATGTATATTCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
*
71217 ACATATATGTATATGCATAACAAATTTATAATTAATTT
1 ACATACATGTATATGCATAACAAATTTATAATTAATTT
71255 A
1 A
71256 TAATTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (38 bp):
ACATACATGTATATGCATAACAAATTTATAATTAATTT
Found at i:71253 original size:11 final size:11
Alignment explanation
Indices: 71239--71276 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
71229 ATGCATAACA
71239 AATTTATAATT
1 AATTTATAATT
71250 AATTTATAATT
1 AATTTATAATT
71261 -ATTTAATAATT
1 AATTT-ATAATT
*
71272 TATTT
1 AATTT
71277 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:72020 original size:135 final size:135
Alignment explanation
Indices: 71778--72038 Score: 443
Period size: 135 Copynumber: 1.9 Consensus size: 135
71768 TGAAAATATT
*
71778 ATTAATTTAATTAGATTATATTAGAATTAAAATAAATTTACTTACAACCAATTAATTTTAGACAA
1 ATTAATTTAATTAGATTATATTAGAATTAAAATAAATTTACTCACAACCAATTAATTTTAGACAA
* *
71843 ATGTCGAAATGAGAGAAACCAAATACTGAGTATACAGTAGTTTGAGGATAACTTTAATAGTAGGG
66 ATGTCGAAATGAGAGAAACCAAATACTGAGCATACAGCAGTTTGAGGATAACTTTAATAGTAGGG
71908 TATAG
131 TATAG
*
71913 ATTAATTTAATTAGATTATATTAGAATTAAAATAAATTTACTCATAACCAATTAATTTTAGACAA
1 ATTAATTTAATTAGATTATATTAGAATTAAAATAAATTTACTCACAACCAATTAATTTTAGACAA
* * *
71978 ATGTCGAAA-GCAGAGAAACTAAATACTTAGCATATAGCAGTTTGAGGATAACTTTAATAGT
66 ATGTCGAAATG-AGAGAAACCAAATACTGAGCATACAGCAGTTTGAGGATAACTTTAATAGT
72039 CGAAAGGAGA
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
134 1 0.01
135 117 0.99
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (135 bp):
ATTAATTTAATTAGATTATATTAGAATTAAAATAAATTTACTCACAACCAATTAATTTTAGACAA
ATGTCGAAATGAGAGAAACCAAATACTGAGCATACAGCAGTTTGAGGATAACTTTAATAGTAGGG
TATAG
Found at i:72044 original size:57 final size:57
Alignment explanation
Indices: 71980--72095 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
71970 TTAGACAAAT
* * *
71980 GTCGAAAGCAGAGAAACTAAATACTTAGCATATAGCAGTTTGAGGATAACTTTAATA
1 GTCGAAAGCAGAGAAACTAAATACTTAACATACAACAGTTTGAGGATAACTTTAATA
* *
72037 GTCGAAAGGAGAGAAACTAAATACTTAACATACAACAGTTTGGGGATAACTTTAATA
1 GTCGAAAGCAGAGAAACTAAATACTTAACATACAACAGTTTGAGGATAACTTTAATA
72094 GT
1 GT
72096 AAAGTATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (57 bp):
GTCGAAAGCAGAGAAACTAAATACTTAACATACAACAGTTTGAGGATAACTTTAATA
Found at i:73766 original size:107 final size:107
Alignment explanation
Indices: 73593--73963 Score: 622
Period size: 107 Copynumber: 3.5 Consensus size: 107
73583 AGTTTAGCCT
73593 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAA-TTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
* *
73658 TAATAATTTATTGTTATAGAGTTTTAGAAATGAAATACAAAAC
65 TAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
73701 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
73766 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * *
73808 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGAGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
* *
73873 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
73913 TAA-TTCACTAAGTTTAGCCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
73964 TAGAAAAATT
Statistics
Matches: 252, Mismatches: 11, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
104 44 0.17
105 36 0.14
107 141 0.56
108 31 0.12
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:82895 original size:30 final size:30
Alignment explanation
Indices: 82860--82933 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
82850 AGCATAACTT
82860 AACATGGCCCGATCCAAGTACCAAAAAAGG
1 AACATGGCCCGATCCAAGTACCAAAAAAGG
*
82890 AACATGGCCCGATCCAAGTTCCAAAAAAGG
1 AACATGGCCCGATCCAAGTACCAAAAAAGG
82920 AACATGGCCCGATC
1 AACATGGCCCGATC
82934 TGGCCCAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.12
Consensus pattern (30 bp):
AACATGGCCCGATCCAAGTACCAAAAAAGG
Found at i:86388 original size:14 final size:14
Alignment explanation
Indices: 86369--86397 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
86359 ATGGAAGAGG
86369 GGAAAAAAAGAAAA
1 GGAAAAAAAGAAAA
86383 GGAAAAAAAGAAAA
1 GGAAAAAAAGAAAA
86397 G
1 G
86398 CAATCTCATC
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
GGAAAAAAAGAAAA
Done.