Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014182.1 Corchorus capsularis cultivar CVL-1 contig14203, 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: 33556
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:818 original size:16 final size:16
Alignment explanation
Indices: 797--838 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
787 CCGTCCGAAT
*
797 CCGAATCCGAAATTAC
1 CCGAATCCGAAAATAC
* *
813 CCGAATTCGAAAATAT
1 CCGAATCCGAAAATAC
829 CCGAATCCGA
1 CCGAATCCGA
839 GACAACCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (16 bp):
CCGAATCCGAAAATAC
Found at i:861 original size:16 final size:16
Alignment explanation
Indices: 842--872 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
832 AATCCGAGAC
842 AACCCGAACCCGTCCG
1 AACCCGAACCCGTCCG
858 AACCCGAACCCGTCC
1 AACCCGAACCCGTCC
873 CCGAGATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.52, G:0.16, T:0.06
Consensus pattern (16 bp):
AACCCGAACCCGTCCG
Found at i:1657 original size:23 final size:23
Alignment explanation
Indices: 1611--1665 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1601 TATCGAAACT
1611 GAACCCGAACCCGACCCGGACCC
1 GAACCCGAACCCGACCCGGACCC
* *
1634 GAACTCGAACCCGATCC-GAGCCC
1 GAACCCGAACCCGACCCGGA-CCC
*
1657 GAATCCGAA
1 GAACCCGAA
1666 AATACCCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.29, C:0.44, G:0.22, T:0.05
Consensus pattern (23 bp):
GAACCCGAACCCGACCCGGACCC
Found at i:1675 original size:16 final size:16
Alignment explanation
Indices: 1654--1723 Score: 99
Period size: 16 Copynumber: 4.4 Consensus size: 16
1644 CCGATCCGAG
*
1654 CCCGAATCCGAAAATA
1 CCCGAACCCGAAAATA
1670 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
*
1685 CCCGAACCC-AACAAAA
1 CCCGAACCCGAA-AATA
1701 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
1717 CCCGAAC
1 CCCGAAC
1724 TCGTCCGAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 15 0.31
16 31 0.65
17 2 0.04
ACGTcount: A:0.43, C:0.40, G:0.11, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:1681 original size:6 final size:6
Alignment explanation
Indices: 1611--1665 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1601 TATCGAAACT
* * * *
1611 GAACCC GAACCC G-ACCC GGACCC GAACTC GAACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
*
1657 GAATCC GAA
1 GAACCC GAA
1666 AATACCCGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.29, C:0.44, G:0.22, T:0.05
Consensus pattern (6 bp):
GAACCC
Found at i:6540 original size:21 final size:21
Alignment explanation
Indices: 6514--6567 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
6504 TTTTTAGCTT
*
6514 ATGAAAAACATGAGATAATTG
1 ATGAAAAACATGAGATAATTC
*****
6535 ATGAAATTGGCGAGATAATTC
1 ATGAAAAACATGAGATAATTC
6556 ATGAAAAACATG
1 ATGAAAAACATG
6568 TTTCACCTAA
Statistics
Matches: 22, Mismatches: 11, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGAAAAACATGAGATAATTC
Found at i:12696 original size:17 final size:17
Alignment explanation
Indices: 12670--12712 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
12660 ATTCATGTAG
*
12670 TTCCAATAGGATTGCAT
1 TTCCAGTAGGATTGCAT
12687 TTCCAGTAGGATTGCAT
1 TTCCAGTAGGATTGCAT
12704 TTCCAGTAG
1 TTCCAGTAG
12713 ATAATTGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (17 bp):
TTCCAGTAGGATTGCAT
Found at i:12870 original size:11 final size:11
Alignment explanation
Indices: 12854--12878 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12844 GCAAATAATT
12854 GAAGCATTTTA
1 GAAGCATTTTA
12865 GAAGCATTTTA
1 GAAGCATTTTA
12876 GAA
1 GAA
12879 TTAAGGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (11 bp):
GAAGCATTTTA
Found at i:16656 original size:2 final size:2
Alignment explanation
Indices: 16649--16678 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16639 CCTATAGTGA
16649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16679 TATTGGGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19888 original size:41 final size:41
Alignment explanation
Indices: 19831--19910 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
19821 TAGTTAAAAT
19831 CTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAAC
1 CTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAAC
*
19872 CTTAATTCAGTGTAATTAAGAGGTAATTAGGAAAGTCAA
1 CTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAA
19911 GGTAAGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (41 bp):
CTTAATTCAGTGTAATTAAGAGGTAATTAAGAAAGTCAAAC
Found at i:20066 original size:70 final size:70
Alignment explanation
Indices: 19918--20123 Score: 200
Period size: 70 Copynumber: 2.9 Consensus size: 70
19908 CAAGGTAAGT
* * * * ***
19918 AAAGTCAAGGTCTCAATTTAGCAATTAAGAAGAGTAAAGTCTTAATTCTGGGTAATTAAGAGGGG
1 AAAGTCAAGGTCTTAATTTGGCAATCAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAG
19983 AAAGC
66 AAAGC
* * * *
19988 AAAATCAAGGTCTTAATTTGGCAATCAAGAATAGTAAATTCTTAATTCAGGGTAGTTAAGAAAAG
1 AAAGTCAAGGTCTTAATTTGGCAATCAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAG
20053 AAAGTC
66 AAAG-C
* * * * * * * *
20059 -CAGTCAAGGCCCTAATTTGGGTAATTAAGGAAG-GTAACGTCTTAATTCAAGGCAATTAAGAAA
1 AAAGTCAAGGTCTTAATTT-GGCAATCAA-GAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAA
20122 AG
64 AG
20124 TATGCATAGT
Statistics
Matches: 110, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
70 72 0.65
71 35 0.32
72 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (70 bp):
AAAGTCAAGGTCTTAATTTGGCAATCAAGAAGAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAG
AAAGC
Found at i:20189 original size:40 final size:40
Alignment explanation
Indices: 20135--20247 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
20125 ATGCATAGTT
* *
20135 AAAGACTTAATTCATAGAAATTAAGTAAAAACAATAGTCA
1 AAAGACTTAATTCATAGAAATTAAGTAAAAACAACAATCA
** * *
20175 AAAGACTTAATTCATAGAAATTAAGTTGAAGCAACAATTA
1 AAAGACTTAATTCATAGAAATTAAGTAAAAACAACAATCA
* * * *
20215 AAAGGCTTAATTCATGGCAATTAAGTAAGAACA
1 AAAGACTTAATTCATAGAAATTAAGTAAAAACA
20248 TTAGAAGACT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (40 bp):
AAAGACTTAATTCATAGAAATTAAGTAAAAACAACAATCA
Found at i:20295 original size:36 final size:36
Alignment explanation
Indices: 20252--20806 Score: 716
Period size: 36 Copynumber: 15.7 Consensus size: 36
20242 AGAACATTAG
* *
20252 AAGACTGACTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
20288 TAGACTGACTTAATTTCAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
20323 AAGACTGACTGAATTTCAAGGAAATTAGGTAAA-AGA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGA-A
* * *
20359 AAGACTGACTTAATTTTAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
20394 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAA-AG
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
20429 AAGACTGACTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
20465 AAGACTGGCTTAGTTTCAAAGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
20501 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
20537 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAATGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
20573 AAGACTGACTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
20609 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * * *
20645 AAGATTGGCTTAGTTTCAAGGAAACTAGGTAGAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
20681 AAGGCTGGCTTAATTTCAAGGAAATTAGGTAATG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
20716 TAGACTGGC-TAGTTTCAAGGAAACTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
20750 AAGATTGGCTTAATTTCAAGGAAATTAAGT--A-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
20783 AAGACAGGCTTAATTTCAAGGAAA
1 AAGACTGGCTTAATTTCAAGGAAA
20807 GAAATTAAGT
Statistics
Matches: 459, Mismatches: 56, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
33 24 0.05
34 29 0.06
35 122 0.27
36 284 0.62
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
Found at i:28916 original size:32 final size:32
Alignment explanation
Indices: 28875--28947 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
28865 TGCAGCAAAA
28875 TAGCGGCGTCTAATG-AGCTAAACGCCACTATT
1 TAGCGGCGTCTAATGAAGC-AAACGCCACTATT
*
28907 TAGCGGCGTCTAATGAAGCAAACGCCGCTATT
1 TAGCGGCGTCTAATGAAGCAAACGCCACTATT
*
28939 TAGTGGCGT
1 TAGCGGCGT
28948 TTAGTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 35 0.92
33 3 0.08
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (32 bp):
TAGCGGCGTCTAATGAAGCAAACGCCACTATT
Found at i:29205 original size:32 final size:32
Alignment explanation
Indices: 29142--29208 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
29132 ATTTCTAAAA
* **
29142 TAGCGGCGTCTGTTTTATTAAACGCCACTATT
1 TAGCGGCGTCTGTTTAAGCAAACGCCACTATT
* **
29174 TAGCGGCGTCTGTTTAAGCAGACGCTGCTATT
1 TAGCGGCGTCTGTTTAAGCAAACGCCACTATT
29206 TAG
1 TAG
29209 TGAAGTCCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (32 bp):
TAGCGGCGTCTGTTTAAGCAAACGCCACTATT
Found at i:30073 original size:2 final size:2
Alignment explanation
Indices: 30066--30090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30056 GATCTTTGCC
30066 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 T
30091 TGTAGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31148 original size:27 final size:27
Alignment explanation
Indices: 31112--31227 Score: 189
Period size: 27 Copynumber: 4.3 Consensus size: 27
31102 TCCGGCTCTC
31112 CCCACTTCGACCGC-AGAAGTGGATCCT
1 CCCACTTCGACC-CAAGAAGTGGATCCT
31139 CCCACTTCGACCCAAGAAGTGGATCCT
1 CCCACTTCGACCCAAGAAGTGGATCCT
* *
31166 ACCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCAAGAAGTGGATCCT
*
31193 CCCACTTCGACCCAAGCAGTGGATCCT
1 CCCACTTCGACCCAAGAAGTGGATCCT
31220 CCCACTTC
1 CCCACTTC
31228 CCCTCGGGTC
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
26 1 0.01
27 82 0.99
ACGTcount: A:0.23, C:0.40, G:0.18, T:0.19
Consensus pattern (27 bp):
CCCACTTCGACCCAAGAAGTGGATCCT
Done.