Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013403.1 Corchorus olitorius cultivar O-4 contig13436, 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: 33055
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:3538 original size:18 final size:18
Alignment explanation
Indices: 3515--3549 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3505 TTTTAGTCAT
*
3515 CTTTGGGCCTTGAAATTG
1 CTTTGGGCCTTAAAATTG
*
3533 CTTTGGGTCTTAAAATT
1 CTTTGGGCCTTAAAATT
3550 AGTTGTTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (18 bp):
CTTTGGGCCTTAAAATTG
Found at i:4451 original size:76 final size:76
Alignment explanation
Indices: 4350--4497 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 76
4340 AAGGAATTTC
* *
4350 CTTCAAAGATTTTCAAATTGGGAAAGATTCCATCAAATTTCCAAGTTTTCAATTTAGGGAAAGAT
1 CTTCAAAGATTTTCAAATTGGGAAAGATCCCATCAAATTTCCAAGATTTCAATTTAGGGAAAGAT
4415 CCCATCAGTTT
66 CCCATCAGTTT
* *
4426 CTTCAAA-ATTTTC-AATTGAGGGAAAGATCCCATCAAGTTTTCAAGATTTCAATTTAGGGAAAG
1 CTTCAAAGATTTTCAAATT--GGGAAAGATCCCATCAAATTTCCAAGATTTCAATTTAGGGAAAG
4489 ATCCCATCA
64 ATCCCATCA
4498 AGTTATCGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
74 4 0.06
75 6 0.09
76 56 0.85
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (76 bp):
CTTCAAAGATTTTCAAATTGGGAAAGATCCCATCAAATTTCCAAGATTTCAATTTAGGGAAAGAT
CCCATCAGTTT
Found at i:4523 original size:38 final size:37
Alignment explanation
Indices: 4359--4584 Score: 231
Period size: 37 Copynumber: 5.9 Consensus size: 37
4349 CCTTCAAAGA
* * * *
4359 TTTTCAAATT-GGGAAAGATTCCATCAAATTTCCAAG
1 TTTTCAATTTAGGGAAAGATCCCATCAAGTTTTCAAG
*
4395 TTTTCAATTTAGGGAAAGATCCCATC-AGTTTCTTCAAAA
1 TTTTCAATTTAGGGAAAGATCCCATCAAG-TT-TTC-AAG
*
4434 TTTTCAATTGAGGGAAAGATCCCATCAAGTTTTCAAG
1 TTTTCAATTTAGGGAAAGATCCCATCAAGTTTTCAAG
* * *
4471 ATTTCAATTTAGGGAAAGATCCCATCAAGTTATCGAAT
1 TTTTCAATTTAGGGAAAGATCCCATCAAGTTTTC-AAG
* **
4509 TTTTCAATTTAGGGAAAAATCCCATCCTGTCTTTTTCAAAG
1 TTTTCAATTTAGGGAAAGATCCCATCAAG---TTTTC-AAG
*
4550 TTTTCAATTTAGGGGAAAGATTCCATCAAAGTTTT
1 TTTTCAATTTA-GGGAAAGATCCCATC-AAGTTTT
4585 TAAAATAGAG
Statistics
Matches: 157, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
36 10 0.06
37 49 0.31
38 32 0.20
39 29 0.18
40 6 0.04
41 17 0.11
42 13 0.08
43 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (37 bp):
TTTTCAATTTAGGGAAAGATCCCATCAAGTTTTCAAG
Found at i:15284 original size:32 final size:33
Alignment explanation
Indices: 15241--15335 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 33
15231 TGTAAGACAT
*
15241 TTAGCGGCGTTTT-TTGTTAGAAACGCCACTAA
1 TTAGTGGCGTTTTATTGTTAGAAACGCCACTAA
*
15273 TTAGTGGCGTTTTACTTG--AGAAATGCCACTAA
1 TTAGTGGCGTTTTA-TTGTTAGAAACGCCACTAA
* *
15305 TTAGTGGCGTTTTACT-TTAAAAACGCCACTA
1 TTAGTGGCGTTTTATTGTTAGAAACGCCACTA
15336 TTATATTAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.02
32 50 0.93
34 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (33 bp):
TTAGTGGCGTTTTATTGTTAGAAACGCCACTAA
Found at i:16554 original size:2 final size:2
Alignment explanation
Indices: 16547--16577 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16537 TATCCCCTCC
16547 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16578 TTGCAATTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19009 original size:32 final size:32
Alignment explanation
Indices: 18966--19026 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
18956 GAAATAACCA
*
18966 AAATAGCGGCGTTTAGGTTCAGAAACGCCGCT
1 AAATAGCGGCGTTTACGTTCAGAAACGCCGCT
* *
18998 AAATAGTGGCGTTTCCGTTCAGAAACGCC
1 AAATAGCGGCGTTTACGTTCAGAAACGCC
19027 AAACATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (32 bp):
AAATAGCGGCGTTTACGTTCAGAAACGCCGCT
Found at i:19091 original size:23 final size:23
Alignment explanation
Indices: 19065--19110 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19055 TTCTGTACGG
19065 AAACGCCACTATTTAGCGGCGTT
1 AAACGCCACTATTTAGCGGCGTT
* *
19088 AAACGCCGCTATTTAGTGGCGTT
1 AAACGCCACTATTTAGCGGCGTT
19111 TCTGAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
AAACGCCACTATTTAGCGGCGTT
Found at i:21385 original size:2 final size:2
Alignment explanation
Indices: 21378--21406 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21368 GTTCATAGTT
21378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21407 TTTTTGTGTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27609 original size:41 final size:42
Alignment explanation
Indices: 27543--27915 Score: 342
Period size: 41 Copynumber: 8.8 Consensus size: 42
27533 GCCATATAGA
* *
27543 AATTGCCCTTGTGTTATAATTGTGTTTAGGGACTTTA-ATATG
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAGATATG
* * * *
27585 TA-TGCCTCTGTGTTATAAATGTGTTTGATGACTTTTAGAGA-G
1 AATTGCCCCTGTGTTATAAATGTGTTTG-GGAC-TTTAGATATG
*
27627 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTG-TAT-
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAGATATG
* *
27668 AGA-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAGAGA-G
1 A-ATTGCCCCTGTGTTATAAATGTGTTTG-GGAC-TTTAGATATG
*
27711 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTG-TAT-
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAGATATG
* * * *
27752 AGA-TGCCTCTGTGTTAT-AATGTGTTTGAAGACTTTAGAAAGAG
1 A-ATTGCCCCTGTGTTATAAATGTGTTTG-GGACTTTAGATA-TG
*
27795 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT-TATAT-
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTTAGATATG
* * *
27836 AGA-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAAAGAG
1 A-ATTGCCCCTGTGTTATAAATGTGTTTG-GGACTTTAGATA-TG
27880 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATAAATGTGTTT-GGGACTTT
27916 GGTTATTGGG
Statistics
Matches: 270, Mismatches: 32, Indels: 56
0.75 0.09 0.16
Matches are distributed among these distances:
39 1 0.00
40 19 0.07
41 100 0.37
42 26 0.10
43 74 0.27
44 48 0.18
45 2 0.01
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.41
Consensus pattern (42 bp):
AATTGCCCCTGTGTTATAAATGTGTTTGGGACTTTAGATATG
Found at i:27647 original size:43 final size:44
Alignment explanation
Indices: 27587--27915 Score: 398
Period size: 43 Copynumber: 7.8 Consensus size: 44
27577 TTAATATGTA
* *
27587 TGCCTCTGTGTTATAAATGTGTTTGATGACTTTTAG-AGAGAAT
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAGAAGAGAAT
* * *
27630 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTT-GTATAG-A-
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAGAAGAGAAT
*
27671 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAG-AGAGAAT
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAGAAGAGAAT
* * *
27714 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTT-GTATAG-A-
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAGAAGAGAAT
* *
27755 TGCCTCTGTGTTAT-AATGTGTTTGAAGAC-TTTAGAAAGAGAAT
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAG-AAGAGAAT
* * *
27798 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTA-TATAG-A-
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAGAAGAGAAT
*
27839 TGCCTCTGTGTTATAAATGTGTTTGAGGAC-TTTAGAAAGAGAAT
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAG-AAGAGAAT
*
27883 TGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTT
27916 GGTTATTGGG
Statistics
Matches: 244, Mismatches: 26, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
39 3 0.01
40 18 0.07
41 79 0.32
42 11 0.05
43 86 0.35
44 41 0.17
45 6 0.02
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (44 bp):
TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAGAAGAGAAT
Found at i:27684 original size:84 final size:84
Alignment explanation
Indices: 27543--27915 Score: 601
Period size: 84 Copynumber: 4.4 Consensus size: 84
27533 GCCATATAGA
* * * *
27543 AATTGCCCTTGTGTTATAATTGTGTTTAGGGACTTTAATAT-GTATGCCTCTGTGTTATAAATGT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTATATAG-ATGCCTCTGTGTTATAAATGT
*
27607 GTTTGATGACTTTTAG-AGAG
65 GTTTGAGGAC-TTTAGAAGAG
*
27627 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTGTATAGATGCCTCTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTATATAGATGCCTCTGTGTTATAAATGTG
27692 TTTGAGGACTTTTAG-AGAG
66 TTTGAGGAC-TTTAGAAGAG
*
27711 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTGTATAGATGCCTCTGTGTTAT-AATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTATATAGATGCCTCTGTGTTATAAATGTG
*
27775 TTTGAAGACTTTAGAAAGAG
66 TTTGAGGACTTTAG-AAGAG
27795 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTATATAGATGCCTCTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTATATAGATGCCTCTGTGTTATAAATGTG
27860 TTTGAGGACTTTAGAAAGAG
66 TTTGAGGACTTTAG-AAGAG
27880 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
27916 GGTTATTGGG
Statistics
Matches: 276, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
82 5 0.02
83 14 0.05
84 195 0.71
85 62 0.22
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.41
Consensus pattern (84 bp):
AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTTATATAGATGCCTCTGTGTTATAAATGTG
TTTGAGGACTTTAGAAGAG
Found at i:28297 original size:18 final size:18
Alignment explanation
Indices: 28257--28303 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
28247 TTAATCAATC
* *
28257 ACTTGCTTAATTCCTTTT
1 ACTTGCTTAATTCATGTT
28275 ACTTGCTTAATTACATGTT
1 ACTTGCTTAATT-CATGTT
28294 -CTTGCTTAAT
1 ACTTGCTTAAT
28304 CAGTTTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (18 bp):
ACTTGCTTAATTCATGTT
Found at i:28390 original size:24 final size:23
Alignment explanation
Indices: 28358--28404 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
28348 ATTTGCTAAC
28358 TTATTCAATTTAGCAGAAAGCTTT
1 TTATTCAATTTAGCAG-AAGCTTT
28382 TTATTCAATTTAGCAGAAGCTTT
1 TTATTCAATTTAGCAGAAGCTTT
28405 CATAATACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (23 bp):
TTATTCAATTTAGCAGAAGCTTT
Found at i:28657 original size:20 final size:20
Alignment explanation
Indices: 28634--28672 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28624 AAACACAACT
* *
28634 CAAATAACATGAACAAATCG
1 CAAACAACAAGAACAAATCG
*
28654 CAAACAACAAGAGCAAATC
1 CAAACAACAAGAACAAATC
28673 AGGAAGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.10
Consensus pattern (20 bp):
CAAACAACAAGAACAAATCG
Found at i:29293 original size:21 final size:21
Alignment explanation
Indices: 29269--29317 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29259 TTGCATACTT
*
29269 TTCAATTGATTGAAACTTAAC
1 TTCAATCGATTGAAACTTAAC
* *
29290 TTCAATCGATTGGACCTTAAC
1 TTCAATCGATTGAAACTTAAC
*
29311 ATCAATC
1 TTCAATC
29318 CACTACAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (21 bp):
TTCAATCGATTGAAACTTAAC
Done.