Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013573.1 Corchorus olitorius cultivar O-4 contig13606, 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: 15292
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:3183 original size:13 final size:14
Alignment explanation
Indices: 3142--3185 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
3132 CTAAATTGAC
3142 ATTATTAAAATTT-
1 ATTATTAAAATTTA
*
3155 ATTATTTAAAAATTA
1 ATTA-TTAAAATTTA
3170 ATTA-TAAAATTTA
1 ATTATTAAAATTTA
3183 ATT
1 ATT
3186 TAGACCGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 15 0.56
14 8 0.30
15 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:3664 original size:22 final size:22
Alignment explanation
Indices: 3636--3698 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
3626 TGTCTCTGTG
3636 TGGTTATTAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAAGA
* *
3658 TGGTTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AAGA
* *
3681 -GGTTATCAAAATTCCATA
1 TGGTTATTAAAATTTCATA
3699 GTGTGATTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 31 0.89
23 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAAGA
Found at i:3787 original size:22 final size:22
Alignment explanation
Indices: 3633--3849 Score: 70
Period size: 22 Copynumber: 9.8 Consensus size: 22
3623 TCTTGTCTCT
* *
3633 GTGTGGTTATTAAAATTTCATAA
1 GTGTGGTTATCAAAATTCCAT-A
* * * *
3656 G-ATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTCCAT-A
*
3678 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTCCATA
* * *
3699 GTGTGATTACCAAAATTCAATA
1 GTGTGGTTATCAAAATTCCATA
**
3721 -TG-GAAGTTATCAAAATTTTAT-
1 GTGTG--GTTATCAAAATTCCATA
* * * **
3742 GGGAAGCTTATCAAAATTGTATA
1 GTG-TGGTTATCAAAATTCCATA
*
3765 GTGTGGTTACCAAAATTCCATA
1 GTGTGGTTATCAAAATTCCATA
* * *
3787 G-GATCAGGTTATTAAAATTTCTTA
1 GTG-T--GGTTATCAAAATTCCATA
* ** *
3811 G-GAAGGTTATTGAAATTTCATA
1 GTG-TGGTTATCAAAATTCCATA
*
3833 GTGTGGTTATCACAATT
1 GTGTGGTTATCAAAATT
3850 TTATAGAAAG
Statistics
Matches: 147, Mismatches: 36, Indels: 23
0.71 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 5 0.03
22 119 0.81
23 4 0.03
24 18 0.12
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTCCATA
Found at i:3803 original size:24 final size:22
Alignment explanation
Indices: 3776--3833 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
3766 TGTGGTTACC
*
3776 AAAATTCCATAGGATCAGGTTATT
1 AAAATTTCATAGGA--AGGTTATT
*
3800 AAAATTTCTTAGGAAGGTTATT
1 AAAATTTCATAGGAAGGTTATT
*
3822 GAAATTTCATAG
1 AAAATTTCATAG
3834 TGTGGTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.60
24 12 0.40
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATT
Found at i:3898 original size:22 final size:22
Alignment explanation
Indices: 3873--4766 Score: 231
Period size: 22 Copynumber: 40.7 Consensus size: 22
3863 TTCAAAGAGA
* *
3873 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
3895 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* **
3917 TTAACAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
** * *
3939 TTA-CTACTATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
3961 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
3983 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
4005 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
4030 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * * *
4052 TTATC-GAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
4073 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
* *
4097 ATTATCAAAATTT-ATA-AGA-A
1 -TTATCAAAATTTCATAGTGAGG
* * * *
4117 TTATCAAAATATCAAAGCGAGA
1 TTATCAAAATTTCATAGTGAGG
* * *
4139 TTATCAAAATTAT-ATAATGTGA
1 TTATCAAAATT-TCATAGTGAGG
* *
4161 TTATCAAAATTTCATAGAGCGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
4183 TCAACAAAATTTTATAGAGATG
1 TTATCAAAATTTCATAGTGAGG
**
4205 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
4227 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* **
4249 TTACCAAAATTTCATAGTGTAAT
1 TTATCAAAATTTCATAGTG-AGG
* ** ** * * *
4272 TTCTGGGGAGGTTATCAAAAT-ATG
1 TTAT--CAAAATT-TCATAGTGAGG
** * *
4296 AAAACCAAA--T--TAG-GAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
4314 TTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
* *
4336 TAATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* *
4358 TTTTCAAAATTTCATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
*
4380 TTATCAAAATTTCATACG-GAGA
1 TTATCAAAATTTCATA-GTGAGG
** *
4402 TTAAAAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
** *
4424 TTATCAAAAAATCATAG-GAAAG
1 TTATCAAAATTTCATAGTG-AGG
4446 TTATCAAAA--TC-T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
*
4462 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
4484 TTATCAAAGTTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
4506 TTTATCAAGATTTTATAG-GAAGG
1 -TTATCAAAATTTCATAGTG-AGG
* ** *
4529 TTTATCAAAATTTTATAACGAGA
1 -TTATCAAAATTTCATAGTGAGG
* * *
4552 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
4574 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
4596 TTA-CTAACAA-TTCATA-TGGAGG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * * ** *
4618 TTTTTAAATTTTCACAACGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
4640 TTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
4662 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
4685 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCATAGTGAGG
4707 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
4729 TCT-TCAAAATTTCTTAGGGAGG
1 T-TATCAAAATTTCATAGTGAGG
**
4751 TTAAGAAAATTTCATA
1 TTATCAAAATTTCATA
4767 AGAAGGTTAA
Statistics
Matches: 634, Mismatches: 170, Indels: 136
0.67 0.18 0.14
Matches are distributed among these distances:
16 9 0.01
17 2 0.00
18 8 0.01
19 14 0.02
20 14 0.02
21 33 0.05
22 440 0.69
23 74 0.12
24 6 0.01
25 19 0.03
26 11 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:4519 original size:23 final size:23
Alignment explanation
Indices: 4462--4545 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
4452 AAATCTGTAG
* *
4462 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAGATTTTATAGGGAGGT
4484 TTATCAA-AGTTTTATAGGGAGGT
1 TTATCAAGA-TTTTATAGGGAGGT
*
4507 TTATCAAGATTTTATAGGAAGGT
1 TTATCAAGATTTTATAGGGAGGT
*
4530 TTATCAAAATTTTATA
1 TTATCAAGATTTTATA
4546 ACGAGATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
21 1 0.02
22 18 0.33
23 35 0.64
24 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
TTATCAAGATTTTATAGGGAGGT
Found at i:4556 original size:45 final size:45
Alignment explanation
Indices: 4462--4585 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
4452 AAATCTGTAG
* ** *
4462 TTATCAAGATTTCATAAGGAGGTTATCAAAGTTTTATAGGGAGGT
1 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAACGAGGA
*
4507 TTATCAAGATTTTAT-AGGAAGGTTTATCAAAATTTTATAACGA-GA
1 TTATCAAGATTTCATAAGG-AGG-TTATCAAAATTTTATAACGAGGA
* *
4552 TTATCACA-ATTTCAT-AGTGTGATTATCAAAATTT
1 TTATCA-AGATTTCATAAG-GAGGTTATCAAAATTT
4586 CAGAGTGTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 15 0.22
45 33 0.49
46 19 0.28
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (45 bp):
TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAACGAGGA
Found at i:4773 original size:22 final size:22
Alignment explanation
Indices: 4734--4795 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
4724 TGAGGTCTTC
* * * *
4734 AAAATTTCTTAGGGAGGTTAAG
1 AAAATTTCATAAGAAGGTTAAA
4756 AAAATTTCATAAGAAGGTTAAA
1 AAAATTTCATAAGAAGGTTAAA
* *
4778 AAAAATT-ATAAAAAGGTT
1 AAAATTTCATAAGAAGGTT
4796 CTCGAAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTTAAA
Found at i:6122 original size:24 final size:24
Alignment explanation
Indices: 6071--6122 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
6061 AAAAATACCC
*
6071 AAATTACAAATAAAAAGAAAAAGG
1 AAATTACAAATAAAAAGAAAAAGA
* *
6095 AAATTACAAAATGAATAGAAAAA-A
1 AAATTAC-AAATAAAAAGAAAAAGA
6119 AAAT
1 AAAT
6123 GCAGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.15
Consensus pattern (24 bp):
AAATTACAAATAAAAAGAAAAAGA
Found at i:6947 original size:20 final size:22
Alignment explanation
Indices: 6924--6964 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6914 TCGAGCTCGG
6924 CTCGAA-TTTTC-CGAGTCGAA
1 CTCGAATTTTTCTCGAGTCGAA
6944 CTCGAATTTTTCTCGAGTCGA
1 CTCGAATTTTTCTCGAGTCGA
6965 GCCCGAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
CTCGAATTTTTCTCGAGTCGAA
Found at i:8862 original size:138 final size:138
Alignment explanation
Indices: 8614--8864 Score: 322
Period size: 138 Copynumber: 1.8 Consensus size: 138
8604 CACTGACAAT
* * * * *
8614 GCCCTTTCCTTTTCAACTTCTGTTTCTAATGAATCGATCTTTGAAGACATTGTGAGAGCCTCTGC
1 GCCCTTTCCTTTTCAACTTCAGCTTCTAATGAATCGATCTTTGAAGACATTGTCACAGCATCTGC
* *
8679 TTCAATGCTAATGAGTTGAGACTCAAGAAGTTGCTTCGCTTCATTTGCATCAGCTGAAACTTGCG
66 TTCAATGCTAATGAGTTGAGACTCAAGAAGCTCCTTCGCTTCATTTGCATCAGCTGAAACTTGCG
8744 CCGATAAG
131 CCGATAAG
* * * ** * * * *
8752 GCCCTTTCCTTTTCAATTTCAGCTTCTAATGAGTTGATCTTTGCTGACATTGTCTCTGTATCTGT
1 GCCCTTTCCTTTTCAACTTCAGCTTCTAATGAATCGATCTTTGAAGACATTGTCACAGCATCTGC
* * * *
8817 TTCCATGCTACTGAGTTGAGACTCAAGATGCTCCTTTGCTTCATTTGC
66 TTCAATGCTAATGAGTTGAGACTCAAGAAGCTCCTTCGCTTCATTTGC
8865 CATGGACAGC
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
138 93 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (138 bp):
GCCCTTTCCTTTTCAACTTCAGCTTCTAATGAATCGATCTTTGAAGACATTGTCACAGCATCTGC
TTCAATGCTAATGAGTTGAGACTCAAGAAGCTCCTTCGCTTCATTTGCATCAGCTGAAACTTGCG
CCGATAAG
Found at i:9191 original size:126 final size:126
Alignment explanation
Indices: 8964--9337 Score: 685
Period size: 126 Copynumber: 3.0 Consensus size: 126
8954 TGAGAGCGAT
8964 CTCTAGTTCAGCCTTCTCAAGTTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
1 CTCTAGTTCAGCCTTCTCAAGTTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
* * * *
9029 TCATGGCTTCGAGTTCAGCCTTTAATGAGTTGTCACTATCATTAGATTGTTCGGCAGATTG
66 TCATGGCTTCAAGTTCAGCCTTTAATGAGTTATCACTATCATTACATTGTTCGGCAGATCG
*
9090 CTCTAGTTCAGCCTTCTCAAATTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
1 CTCTAGTTCAGCCTTCTCAAGTTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
*
9155 TCATGGCTTCAAGTTCAGCCTTTAATGAGTTATCACTATCATTACATTGTTTGGCAGATCG
66 TCATGGCTTCAAGTTCAGCCTTTAATGAGTTATCACTATCATTACATTGTTCGGCAGATCG
*
9216 CTCTAATTCAGCCTTCTCAAGTTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
1 CTCTAGTTCAGCCTTCTCAAGTTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
9281 TCATGGCTTCAAGTTCAGCCTTTAATGAGTTATCACTATCATTACATTGTTCGGCAG
66 TCATGGCTTCAAGTTCAGCCTTTAATGAGTTATCACTATCATTACATTGTTCGGCAG
9338 TAGCTTTTGA
Statistics
Matches: 239, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 239 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (126 bp):
CTCTAGTTCAGCCTTCTCAAGTTCAATCTTCTCCAATTTCTCTTCAAGTTCCGCTGTTCGATGAA
TCATGGCTTCAAGTTCAGCCTTTAATGAGTTATCACTATCATTACATTGTTCGGCAGATCG
Found at i:14461 original size:31 final size:31
Alignment explanation
Indices: 14423--14483 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
14413 CAAAACTTAC
*
14423 TTCGAA-TTCTTTTCACTCAATTCAGTAAGCG
1 TTCGAATTTCTTTT-ACTCAATTCAATAAGCG
14454 TTCGAATTTCTTTTACTCAATTCAATAAGC
1 TTCGAATTTCTTTTACTCAATTCAATAAGC
14484 TTTGGTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (31 bp):
TTCGAATTTCTTTTACTCAATTCAATAAGCG
Done.